From 8f1c9925f4efc5dd9f01f25bbe76418caf39be09 Mon Sep 17 00:00:00 2001 From: rnfinnegan Date: Mon, 20 Feb 2023 16:30:20 +1100 Subject: [PATCH 01/32] update vis bug fixes --- platipy/imaging/visualisation/visualiser.py | 249 ++++++++++++++------ 1 file changed, 172 insertions(+), 77 deletions(-) diff --git a/platipy/imaging/visualisation/visualiser.py b/platipy/imaging/visualisation/visualiser.py index 2db2ec5f..f4053bc1 100644 --- a/platipy/imaging/visualisation/visualiser.py +++ b/platipy/imaging/visualisation/visualiser.py @@ -17,7 +17,9 @@ import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec -#from mpl_toolkits.axes_grid1 import make_axes_locatable # , AxesGrid, ImageGrid +import matplotlib.colors as colors + +# from mpl_toolkits.axes_grid1 import make_axes_locatable # , AxesGrid, ImageGrid import numpy as np import SimpleITK as sitk @@ -218,6 +220,7 @@ def add_scalar_overlay( min_value=False, max_value=False, discrete_levels=False, + show_as_contours=False, mid_ticks=False, show_colorbar=True, norm=None, @@ -256,6 +259,7 @@ def add_scalar_overlay( min_value=min_value, max_value=max_value, discrete_levels=discrete_levels, + show_as_contours=show_as_contours, mid_ticks=mid_ticks, show_colorbar=show_colorbar, norm=norm, @@ -278,6 +282,7 @@ def add_scalar_overlay( min_value=min_value, max_value=max_value, discrete_levels=discrete_levels, + show_as_contours=show_as_contours, mid_ticks=mid_ticks, show_colorbar=show_colorbar, norm=norm, @@ -443,9 +448,9 @@ def show(self, interact=False): self._overlay_comparison() self._overlay_scalar_field() - self._overlay_vector_field() self._overlay_contours() self._overlay_bounding_boxes() + self._overlay_vector_field() self._adjust_view() @@ -485,8 +490,8 @@ def _display_slice(self): window = (lower, upper - lower) try: logger.info( - "Found a (z,y,x,%s) dimensional array - assuming this is an RGB" - "image.", nda.shape[3] + "Found a (z,y,x,%s) dimensional array - assuming this is an RGB" "image.", + nda.shape[3], ) nda /= nda.max() except ValueError: @@ -977,7 +982,8 @@ def _adjust_view(self): y_0, y_1 = sorted([y_0, y_1]) if self.__axis == "z" and self.__origin == "normal": - y_0, y_1 = y_1, y_0 + y_1, y_0 = self.__image.GetSize()[0] - y_0, self.__image.GetSize()[0] - y_1 + # I don't know why I put this in ratio_x = np.abs(x_1 - x_0) / np.abs(x_orig_1 - x_orig_0) ratio_y = np.abs(y_1 - y_0) / np.abs(y_orig_1 - y_orig_0) @@ -1066,6 +1072,7 @@ def _overlay_contours(self): linestyles=ls_dict[c_name], extent=extent_dict[self.__axis], origin=origin, + zorder=0, ) ax.plot( [0], @@ -1189,12 +1196,15 @@ def _overlay_scalar_field(self): else: s_min = nda.min() - if scalar.discrete_levels: - colormap_name = scalar.colormap.name - colormap = plt.cm.get_cmap(colormap_name, scalar.discrete_levels) + colormap_name = scalar.colormap.name + colormap = plt.cm.get_cmap(colormap_name) - else: - colormap = scalar.colormap + if scalar.discrete_levels or scalar.show_as_contours: + if not scalar.discrete_levels: + scalar.discrete_levels = 10 + + colormap = plt.cm.get_cmap(colormap_name, scalar.discrete_levels) + contour_levels = scalar.discrete_levels if scalar.norm: norm = scalar.norm @@ -1265,54 +1275,103 @@ def _overlay_scalar_field(self): cor_img = np.ma.masked_less_equal(cor_img, s_min) sag_img = np.ma.masked_less_equal(sag_img, s_min) - ax_view = ax_ax.imshow( - ax_img, - interpolation="none", - cmap=colormap, - clim=(s_min, s_max), - aspect=1, - origin={"normal": "upper", "reversed": "lower"}[self.__origin], - vmin=s_min, - vmax=s_max, - alpha=alpha, - norm=norm, - extent=extent_dict["z"], - ) + if scalar.show_as_contours: - cor_view = ax_cor.imshow( - cor_img, - interpolation="none", - cmap=colormap, - clim=(s_min, s_max), - origin="lower", - aspect=asp, - vmin=s_min, - vmax=s_max, - alpha=alpha, - norm=norm, - extent=extent_dict["y"], - ) + ax_view = ax_ax.contour( + ax_img, + levels=contour_levels, + cmap=colormap, + linewidths=[1], + origin={"normal": "upper", "reversed": "lower"}[self.__origin], + vmin=s_min, + vmax=s_max, + alpha=alpha, + norm=norm, + extent=extent_dict["z"], + ) - sag_view = ax_sag.imshow( - sag_img, - interpolation="none", - cmap=colormap, - clim=(s_min, s_max), - origin="lower", - aspect=asp, - vmin=s_min, - vmax=s_max, - alpha=alpha, - norm=norm, - extent=extent_dict["x"], - ) + # we can't plot colorbars with contour plots + # so we create an equivalent scalar mappable + norm = colors.Normalize(vmin=ax_view.cvalues.min(), vmax=ax_view.cvalues.max()) + + ax_view = plt.cm.ScalarMappable(norm=norm, cmap=ax_view.cmap) + ax_view.set_array([]) + + _ = ax_cor.contour( + cor_img, + levels=contour_levels, + cmap=colormap, + linewidths=[1], + origin="lower", + vmin=s_min, + vmax=s_max, + alpha=alpha, + norm=norm, + extent=extent_dict["y"], + ) + + _ = ax_sag.contour( + sag_img, + levels=contour_levels, + cmap=colormap, + linewidths=[1], + origin="lower", + vmin=s_min, + vmax=s_max, + alpha=alpha, + norm=norm, + extent=extent_dict["x"], + ) - # this is for (work-in-progress) dynamic visualisation - self.__scalar_view = { - "ax_view": ax_view, - "cor_view": cor_view, - "sag_view": sag_view, - } + else: + ax_view = ax_ax.imshow( + ax_img, + interpolation="none", + cmap=colormap, + clim=(s_min, s_max), + aspect=1, + origin={"normal": "upper", "reversed": "lower"}[self.__origin], + vmin=s_min, + vmax=s_max, + alpha=alpha, + norm=norm, + extent=extent_dict["z"], + ) + + cor_view = ax_cor.imshow( + cor_img, + interpolation="none", + cmap=colormap, + clim=(s_min, s_max), + origin="lower", + aspect=asp, + vmin=s_min, + vmax=s_max, + alpha=alpha, + norm=norm, + extent=extent_dict["y"], + ) + + sag_view = ax_sag.imshow( + sag_img, + interpolation="none", + cmap=colormap, + clim=(s_min, s_max), + origin="lower", + aspect=asp, + vmin=s_min, + vmax=s_max, + alpha=alpha, + norm=norm, + extent=extent_dict["x"], + ) + + # this is for (work-in-progress) dynamic visualisation + self.__scalar_view = { + "ax_view": ax_view, + "cor_view": cor_view, + "sag_view": sag_view, + } else: @@ -1341,19 +1400,46 @@ def _overlay_scalar_field(self): origin = "lower" s = return_slice(self.__axis, self.__cut) - ax_view = ax.imshow( - disp_img, - interpolation="none", - cmap=colormap, - clim=(s_min, s_max), - origin=origin, - aspect=asp, - vmin=s_min, - vmax=s_max, - alpha=alpha, - norm=norm, - extent=extent_dict[self.__axis], - ) + + if scalar.show_as_contours: + + _ = ax.contour( + disp_img, + levels=contour_levels, + cmap=colormap, + linewidths=[1], + origin=origin, + vmin=s_min, + vmax=s_max, + alpha=alpha, + norm=norm, + extent=extent_dict[self.__axis], + ) + + # create a scalar mappable for the colorbar + if scalar.norm: + contour_norm = scalar.norm(vmin=s_min, vmax=s_max) + else: + contour_norm = colors.Normalize(vmin=s_min, vmax=s_max) + + ax_view = plt.cm.ScalarMappable(cmap=colormap, norm=contour_norm) + ax_view.set_array([]) + + else: + + ax_view = ax.imshow( + disp_img, + interpolation="none", + cmap=colormap, + clim=(s_min, s_max), + origin=origin, + aspect=asp, + vmin=s_min, + vmax=s_max, + alpha=alpha, + norm=norm, + extent=extent_dict[self.__axis], + ) if scalar.show_colorbar: @@ -1385,7 +1471,7 @@ def _overlay_scalar_field(self): ) # check background values - if np.linalg.norm(colormap(0)[:3]) < 0.1: + if np.linalg.norm(self.__colormap(0)[:3]) < 0.1: # background is dark cbar_color = "white" @@ -1455,13 +1541,14 @@ def _overlay_vector_field(self): if len(axes[:4]) < 4: ax = axes[0] - if hasattr(subsample, "__iter__"): - raise ValueError( - "You have selected an iterable subsampling factor for a\ - single axis. Behaviour undefined in this situation." - ) + if not hasattr(subsample, "__iter__"): + subsample = (subsample,) * 3 + + subsample_img = [ + int(np.ceil((i / j))) for i, j in zip(subsample, image.GetSpacing()[::-1]) + ] - slicer = subsample_vector_field(self.__axis, self.__cut, subsample) + slicer = subsample_vector_field(self.__axis, self.__cut, subsample_img) vector_nda_slice = vector_nda.__getitem__(slicer) vector_ax = vector_nda_slice[:, :, 2].T @@ -1476,7 +1563,11 @@ def _overlay_vector_field(self): invert_field=invert_field, ) - plot_x_loc, plot_y_loc = vector_image_grid(self.__axis, vector_nda, subsample) + plot_x_loc, plot_y_loc = vector_image_grid(self.__axis, vector_nda, subsample_img) + + if self.__origin == "normal" and self.__axis == "z": + plot_y_loc = np.flip(plot_y_loc, 1) + vector_plot_x = -1.0 * vector_plot_x if color_function == "perpendicular": vector_color = vector_plot_z @@ -1561,6 +1652,10 @@ def _overlay_vector_field(self): if min_value is False: min_value = vector_color.min() + if self.__origin == "normal" and im_axis == "z": + plot_y_loc = np.flip(plot_y_loc, 1) + vector_plot_x = -1.0 * vector_plot_x + sp_vector = plot_axes.quiver( plot_x_loc, plot_y_loc, @@ -1606,7 +1701,7 @@ def _overlay_vector_field(self): ) # check background values - if np.linalg.norm(colormap(0)[:3]) < 0.1: + if np.linalg.norm(self.__colormap(0)[:3]) < 0.1: # background is dark cbar_color = "white" From 2d343d0b8299db1f62323b86a1de4bbd5b35849b Mon Sep 17 00:00:00 2001 From: rnfinnegan Date: Mon, 20 Feb 2023 16:38:22 +1100 Subject: [PATCH 02/32] registration and visualisation update --- platipy/imaging/registration/deformable.py | 131 +++++++++++++++------ platipy/imaging/visualisation/utils.py | 4 +- 2 files changed, 100 insertions(+), 35 deletions(-) diff --git a/platipy/imaging/registration/deformable.py b/platipy/imaging/registration/deformable.py index da842bc2..ced1d60c 100644 --- a/platipy/imaging/registration/deformable.py +++ b/platipy/imaging/registration/deformable.py @@ -24,6 +24,9 @@ control_point_spacing_distance_to_number, ) +from platipy.imaging import ImageVisualiser +from platipy.imaging.label.utils import get_com + def multiscale_demons( registration_algorithm, @@ -35,6 +38,7 @@ def multiscale_demons( resolution_staging=None, smoothing_sigmas=None, iteration_staging=None, + interp_order=sitk.sitkLinear, ): """ Run the given registration algorithm in a multiscale fashion. The original scale should not be @@ -60,7 +64,7 @@ def multiscale_demons( fixed_images = [] moving_images = [] - for resolution, smoothing_sigma in reversed(list(zip(resolution_staging, smoothing_sigmas))): + for resolution, smoothing_sigma in zip(resolution_staging, smoothing_sigmas): isotropic_voxel_size_mm = None shrink_factor = None @@ -76,14 +80,17 @@ def multiscale_demons( isotropic_voxel_size_mm=isotropic_voxel_size_mm, shrink_factor=shrink_factor, smoothing_sigma=smoothing_sigma, + interpolator=interp_order, ) ) + moving_images.append( smooth_and_resample( moving_image, isotropic_voxel_size_mm=isotropic_voxel_size_mm, shrink_factor=shrink_factor, smoothing_sigma=smoothing_sigma, + interpolator=interp_order, ) ) @@ -95,51 +102,94 @@ def multiscale_demons( initial_displacement_field = sitk.TransformToDisplacementField( initial_transform, sitk.sitkVectorFloat64, - fixed_images[-1].GetSize(), - fixed_images[-1].GetOrigin(), - fixed_images[-1].GetSpacing(), - fixed_images[-1].GetDirection(), + fixed_image.GetSize(), + fixed_image.GetOrigin(), + fixed_image.GetSpacing(), + fixed_image.GetDirection(), ) else: if len(moving_image.GetSize()) == 2: initial_displacement_field = sitk.Image( - fixed_images[-1].GetWidth(), - fixed_images[-1].GetHeight(), + fixed_image.GetWidth(), + fixed_image.GetHeight(), sitk.sitkVectorFloat64, ) elif len(moving_image.GetSize()) == 3: initial_displacement_field = sitk.Image( - fixed_images[-1].GetWidth(), - fixed_images[-1].GetHeight(), - fixed_images[-1].GetDepth(), + fixed_image.GetWidth(), + fixed_image.GetHeight(), + fixed_image.GetDepth(), sitk.sitkVectorFloat64, ) - initial_displacement_field.CopyInformation(fixed_images[-1]) + initial_displacement_field.CopyInformation(fixed_image) else: - initial_displacement_field = sitk.Resample(initial_displacement_field, fixed_images[-1]) + initial_displacement_field = sitk.Resample( + initial_displacement_field, fixed_image + ) # Run the registration. - iters = iteration_staging[0] - registration_algorithm.SetNumberOfIterations(iters) - initial_displacement_field = registration_algorithm.Execute( - fixed_images[-1], moving_images[-1], initial_displacement_field - ) # Start at the top of the pyramid and work our way down. - for i, (f_image, m_image) in enumerate( - reversed(list(zip(fixed_images[0:-1], moving_images[0:-1]))) - ): - initial_displacement_field = sitk.Resample(initial_displacement_field, f_image) - iters = iteration_staging[i + 1] - registration_algorithm.SetNumberOfIterations(iters) - initial_displacement_field = registration_algorithm.Execute( - f_image, m_image, initial_displacement_field + + dvf_total = sitk.Resample(initial_displacement_field, fixed_image) + + for i in range(len(fixed_images)): + f_image = fixed_images[i] + m_image = moving_images[i] + + # we now apply the (total) transform to the moving image + dvf_total = sitk.Resample(dvf_total, f_image) + + tfm_total = sitk.DisplacementFieldTransform( + sitk.Cast(dvf_total, sitk.sitkVectorFloat64) ) + m_image = sitk.Resample(m_image, tfm_total, interp_order) - output_displacement_field = sitk.Resample( - initial_displacement_field, initial_displacement_field - ) + # set up iteration staging + iters = iteration_staging[i] + registration_algorithm.SetNumberOfIterations(iters) + + # set up regularisation + # leave constant (in image units) for now + + dvf_iter = registration_algorithm.Execute(f_image, m_image) + + # and now add to the running DVF + # importly, at each voxel the deformation vector (source -> destination) + # has to be updated with the vector field itself + dvf_total = dvf_total + sitk.Resample(dvf_iter, tfm_total) - return sitk.DisplacementFieldTransform(initial_displacement_field), output_displacement_field + # manually smooth the DVF + sigma = registration_algorithm.GetStandardDeviations() + dvf_total = sitk.SmoothingRecursiveGaussian(dvf_total, sigma) + dvf_total = sitk.Cast(dvf_total, sitk.sitkVectorFloat64) + + # vis = ImageVisualiser(f_image, cut=get_com(f_image), figure_size_in=6) + # vis.add_comparison_overlay(m_image) + + # vis.add_vector_overlay( + # dvf_iter, + # arrow_scale=0.25, + # arrow_width=0.25, + # subsample=4, + # ) + + # vis.set_limits_from_label(f_image, expansion=100) + # fig = vis.show() + + # test_tfm = sitk.DisplacementFieldTransform( + # sitk.Cast(dvf_iter, sitk.sitkVectorFloat64) + # ) + # test = sitk.Resample(m_image, test_tfm) + + # vis = ImageVisualiser(f_image > 0, cut=get_com(f_image), figure_size_in=6) + # vis.add_comparison_overlay(test > 0) + + # vis.set_limits_from_label(f_image, expansion=100) + # fig = vis.show() + + dvf_total = sitk.Resample(dvf_total, fixed_image) + + return dvf_total def fast_symmetric_forces_demons_registration( @@ -149,6 +199,7 @@ def fast_symmetric_forces_demons_registration( iteration_staging=[10, 10, 10], isotropic_resample=False, initial_displacement_field=None, + regularisation_kernel_mm=1.5, smoothing_sigma_factor=1, smoothing_sigmas=False, default_value=None, @@ -169,6 +220,7 @@ def fast_symmetric_forces_demons_registration( case resolution_staging is used to define voxel size (mm) per level initial_displacement_field (sitk.Image) : Initial displacement field to use + regularisation_kernel_scale (float) : Relative scale (var/voxel size) of the regularisation kernel (Gaussian) ncores (int) : number of processing cores to use smoothing_sigma_factor (float) : the relative width of the Gaussian smoothing kernel interp_order (int) : the interpolation order @@ -200,7 +252,14 @@ def fast_symmetric_forces_demons_registration( registration_method.SetNumberOfThreads(ncores) registration_method.SetSmoothUpdateField(True) registration_method.SetSmoothDisplacementField(True) - registration_method.SetStandardDeviations(1.5) + + # This is the regularisation kernel + # values are set in image (voxel) coordinates + regularisation_kernel_vox = np.array(regularisation_kernel_mm) / np.array( + fixed_image.GetSpacing() + ) + print("regularisation_kernel_vox", regularisation_kernel_vox) + registration_method.SetStandardDeviations(regularisation_kernel_vox.tolist()) # This allows monitoring of the progress if verbose: @@ -212,7 +271,7 @@ def fast_symmetric_forces_demons_registration( if not smoothing_sigmas: smoothing_sigmas = [i * smoothing_sigma_factor for i in resolution_staging] - output_transform, deformation_field = multiscale_demons( + deformation_field = multiscale_demons( registration_algorithm=registration_method, fixed_image=fixed_image, moving_image=moving_image, @@ -221,6 +280,7 @@ def fast_symmetric_forces_demons_registration( iteration_staging=iteration_staging, isotropic_resample=isotropic_resample, initial_displacement_field=initial_displacement_field, + interp_order=interp_order, ) resampler = sitk.ResampleImageFilter() @@ -237,15 +297,18 @@ def fast_symmetric_forces_demons_registration( resampler.SetDefaultPixelValue(default_value) + # create the deformable transform + output_transform = sitk.DisplacementFieldTransform( + sitk.Cast(deformation_field, sitk.sitkVectorFloat64) + ) + resampler.SetTransform(output_transform) registered_image = resampler.Execute(moving_image) registered_image.CopyInformation(fixed_image) registered_image = sitk.Cast(registered_image, moving_image_type) - resampled_field = sitk.Resample(deformation_field, fixed_image) - - return registered_image, output_transform, resampled_field + return registered_image, output_transform, deformation_field def bspline_registration( diff --git a/platipy/imaging/visualisation/utils.py b/platipy/imaging/visualisation/utils.py index 99fcd34f..e7699047 100644 --- a/platipy/imaging/visualisation/utils.py +++ b/platipy/imaging/visualisation/utils.py @@ -57,6 +57,7 @@ def __init__( min_value=False, max_value=False, discrete_levels=False, + show_as_contours=False, mid_ticks=False, show_colorbar=True, norm=None, @@ -69,6 +70,7 @@ def __init__( self.min_value = min_value self.max_value = max_value self.discrete_levels = discrete_levels + self.show_as_contours = show_as_contours self.mid_ticks = mid_ticks self.show_colorbar = show_colorbar self.norm = norm @@ -250,7 +252,7 @@ def reorientate_vector_field(axis, vector_ax, vector_cor, vector_sag, invert_fie if axis == "y": # coronal projection return vector_sag, vector_ax, vector_cor if axis == "z": # axial projection - return vector_sag, -vector_cor, vector_ax + return -vector_sag, -vector_cor, vector_ax return None From 080ec37607a9d4f65a9a9d6efb1891d1561723aa Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 25 May 2023 18:47:05 +0000 Subject: [PATCH 03/32] Bump tornado from 6.2 to 6.3.2 Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.2 to 6.3.2. - [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst) - [Commits](https://github.com/tornadoweb/tornado/compare/v6.2.0...v6.3.2) --- updated-dependencies: - dependency-name: tornado dependency-type: indirect ... 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A good place to start is by looking in the Some examples of what PlatiPy can do: - DICOM organising and converting: * Bulk convert from multiple series and studies with a single function - * Convert DICOM-RT structure and dose filesto NIfTI images + * Convert DICOM-RT structure and dose files to NIfTI images * Create DICOM-RT structure files from binary masks e.g. from automatic contouring algorithms - Image registration * Register images and transform labels with a few lines of code From 0972d72605b96efd3552f1239c0fd19af347ac15 Mon Sep 17 00:00:00 2001 From: Phil Chlap Date: Mon, 26 Jun 2023 22:48:27 +1000 Subject: [PATCH 05/32] Add to README and CITATION.cff --- CITATION.cff | 74 ++++++++++++++++++++++------------------------------ README.md | 60 +++++++++++++++++++++++------------------- 2 files changed, 64 insertions(+), 70 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index fd01ed0a..a5432f8f 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,46 +1,34 @@ -cff-version: 1.2.0 -title: "PlatiPy: Processing Library and Analysis Toolkit for Medical Imaging in Python" -message: >- - If you find the PlatiPy library useful in your research, please consider citing it using these - metadata. -abstract: >- - PlatiPy is a library of tools developed in Python for image processing and analysis of medical - images. A broad scope of functionality is provided including image conversion, registration - and segmentation is provided as well as computation of similarity and radiotherapy dosimtery - metrics and much more. -type: software +cff-version: "1.2.0" authors: - - given-names: Phillip - family-names: Chlap - email: phillip.chlap@unsw.edu.au - affiliation: University of New South Wales +- family-names: Chlap + given-names: Phillip + orcid: "https://orcid.org/0000-0002-6517-8745" +- family-names: Finnegan + given-names: Robert N. + orcid: "https://orcid.org/0000-0003-4728-8462" +doi: 10.5281/zenodo.8032858 +message: If you use this software, please cite our article in the + Journal of Open Source Software. +preferred-citation: + authors: + - family-names: Chlap + given-names: Phillip orcid: "https://orcid.org/0000-0002-6517-8745" - - given-names: Robert - family-names: Finnegan - email: robert.finnegan@sydney.edu.au - affiliation: University of Sydney + - family-names: Finnegan + given-names: Robert N. orcid: "https://orcid.org/0000-0003-4728-8462" -license: Apache-2.0 -repository-code: "https://github.com/pyplati/platipy" -url: "https://pyplati.github.io/platipy/" -keywords: - - "medical image analysis" - - "auto-segmentation" - - "image registration" -references: - - authors: - - family-names: Lowekamp - given-names: Bradley C - - family-names: Chen - given-names: David T - - family-names: Ibáñez - given-names: Luis - - family-names: Blezek - given-names: Daniel - doi: 10.3389/fninf.2013.00045 - issn: 16625196 - journal: "Frontiers in Neuroinformatics" - title: "The design of simpleITK" - type: article - volume: 7 - year: 2013 + date-published: 2023-06-26 + doi: 10.21105/joss.05374 + issn: 2475-9066 + issue: 86 + journal: Journal of Open Source Software + publisher: + name: Open Journals + start: 5374 + title: "PlatiPy: Processing Library and Analysis Toolkit for Medical + Imaging in Python" + type: article + url: "https://joss.theoj.org/papers/10.21105/joss.05374" + volume: 8 +title: "PlatiPy: Processing Library and Analysis Toolkit for Medical + Imaging in Python" \ No newline at end of file diff --git a/README.md b/README.md index cc7e5c58..7ba3f78e 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,15 @@ -# PlatiPy +# PlatiPy + +[![DOI](https://joss.theoj.org/papers/10.21105/joss.05374/status.svg)](https://doi.org/10.21105/joss.05374) + ## Processing Library and Analysis Toolkit for Medical Imaging in Python PlatiPy is a library of **amazing** tools for image processing and analysis - designed specifically -for medical imaging! +for medical imaging! Check out the [PlatiPy documentation](https://pyplati.github.io/platipy/) for more info. -This project was motivated by the need for a simple way to use, visualise, process, and analyse +This project was motivated by the need for a simple way to use, visualise, process, and analyse medical images. Many of the tools and algorithms are designed in the context of radiation therapy, although they are more widely applicable to other fields that use 2D, 3D, or 4D imaging. @@ -16,31 +19,33 @@ We welcome feedback and contributions from the community (yes, you!) and you can information about contributing [here](https://pyplati.github.io/platipy/contributing.html). ## What can I do with **platipy**? -A lot! A good place to start is by looking in the + +A lot! A good place to start is by looking in the [examples directory](https://github.com/pyplati/platipy/tree/master/examples). Some examples of what PlatiPy can do: - - DICOM organising and converting: - * Bulk convert from multiple series and studies with a single function - * Convert DICOM-RT structure and dose files to NIfTI images - * Create DICOM-RT structure files from binary masks e.g. from automatic contouring algorithms - - Image registration - * Register images and transform labels with a few lines of code - * Linear transformations: rigid, affine, similarity - * Non-linear deformable transformations: demons, b-splines - * Multiple metrics for optimisation - - Atlas-based segmentation - * A suite of tools that can be used out-of-the-box - * Includes advanced algorithms for - [iterative atlas selection](https://doi.org/10.1088/1361-6560/ab652a/) and + +- DICOM organising and converting: + - Bulk convert from multiple series and studies with a single function + - Convert DICOM-RT structure and dose files to NIfTI images + - Create DICOM-RT structure files from binary masks e.g. from automatic contouring algorithms +- Image registration + - Register images and transform labels with a few lines of code + - Linear transformations: rigid, affine, similarity + - Non-linear deformable transformations: demons, b-splines + - Multiple metrics for optimisation +- Atlas-based segmentation + - A suite of tools that can be used out-of-the-box + - Includes advanced algorithms for + [iterative atlas selection](https://doi.org/10.1088/1361-6560/ab652a/) and [vessel splining](https://doi.org/10.1088/1361-6560/abcb1d/) - - Synthetic deformation field generation - * Simulate anatomically realistic shifts, expansions, and bending - * Compare DIR results from clinical systems - - Basic tools for image processing and analysis - * Computing label similarity metrics: DSC, mean distance to agreement, Hausdorff distance, and more - * Cropping images to a region of interest - * Rotate images and generate maximum/mean intensity projections (beams eye view modelling) +- Synthetic deformation field generation + - Simulate anatomically realistic shifts, expansions, and bending + - Compare DIR results from clinical systems +- Basic tools for image processing and analysis + - Computing label similarity metrics: DSC, mean distance to agreement, Hausdorff distance, and more + - Cropping images to a region of interest + - Rotate images and generate maximum/mean intensity projections (beams eye view modelling) A major part of this package is **visualisation**, and some examples are shown below! @@ -74,7 +79,7 @@ fig = vis.show() ![Figure 2](assets/figure_2.png) #### Calculate deformation vector fields - + ```python from platipy.imaging.registration.deformable import fast_symmetric_forces_demons_registration @@ -99,6 +104,7 @@ fig = vis.show() ![Figure 3](assets/figure_3.png) ## Getting started + There aren't many requirements, just an installed Python interpreter (3.7 or greater). PlatiPy can be installed with **pip**: @@ -117,5 +123,5 @@ pip install platipy[backend] ## Authors -* **Phillip Chlap** - [phillip.chlap@unsw.edu.au](phillip.chlap@unsw.edu.au) -* **Robert Finnegan** - [robert.finnegan@sydney.edu.au](robert.finnegan@sydney.edu.au) +- **Phillip Chlap** - [phillip.chlap@unsw.edu.au](phillip.chlap@unsw.edu.au) +- **Robert Finnegan** - [robert.finnegan@sydney.edu.au](robert.finnegan@sydney.edu.au) From b9118313d569c8854fea5b487ba8ad9a93b83845 Mon Sep 17 00:00:00 2001 From: "S. Gay" Date: Mon, 10 Jul 2023 14:12:26 -0500 Subject: [PATCH 06/32] Replace np.product with np.prod pending deprecation Numpy 1.25 deprecates `np.product` and says to use `np.prod` instead. `np.product` will be fully removed by Numpy v2.0 https://numpy.org/devdocs/release/1.25.0-notes.html#deprecations This change should not break compatibility as `np.prod` has been a method since at least v1.10.1 (probably earlier), while platipy currently requires v1.10.2 as the minimum numpy version https://docs.scipy.org/doc/numpy-1.10.1/reference/generated/numpy.prod.html#numpy.prod Also this change should be purely cosmetic. In the numpy pull request to deprecate `np.product`, it is replaced seamlessly by `np.prod` https://github.com/numpy/numpy/pull/23314/files --- platipy/imaging/dose/dvh.py | 2 +- platipy/imaging/dose/metric.py | 4 ++-- platipy/imaging/label/comparison.py | 4 ++-- platipy/imaging/label/fusion.py | 2 +- platipy/imaging/projects/cardiac/run.py | 6 +++--- platipy/imaging/projects/multiatlas/run.py | 6 +++--- platipy/imaging/utils/valve.py | 2 +- platipy/imaging/utils/ventricle.py | 6 +++--- 8 files changed, 16 insertions(+), 16 deletions(-) diff --git a/platipy/imaging/dose/dvh.py b/platipy/imaging/dose/dvh.py index 8f1d080b..72a88453 100644 --- a/platipy/imaging/dose/dvh.py +++ b/platipy/imaging/dose/dvh.py @@ -87,7 +87,7 @@ def calculate_dvh_for_labels(dose_grid, labels, bin_width=0.1, max_dose=None): mask_array = sitk.GetArrayFromImage(mask) # Compute cubic centimetre volume of structure - cc = mask_array.sum() * np.product([a / 10 for a in mask.GetSpacing()]) + cc = mask_array.sum() * np.prod([a / 10 for a in mask.GetSpacing()]) bins, values = calculate_dvh( dose_grid, labels[k], bins=np.arange(-bin_width / 2, max_dose + bin_width, bin_width) diff --git a/platipy/imaging/dose/metric.py b/platipy/imaging/dose/metric.py index 850600b1..aa7f5256 100644 --- a/platipy/imaging/dose/metric.py +++ b/platipy/imaging/dose/metric.py @@ -72,7 +72,7 @@ def calculate_d_to_volume(dose_grid, label, volume, volume_in_cc=False): mask_array = sitk.GetArrayFromImage(label) if volume_in_cc: - volume = (volume * 1000 / ((mask_array > 0).sum() * np.product(label.GetSpacing()))) * 100 + volume = (volume * 1000 / ((mask_array > 0).sum() * np.prod(label.GetSpacing()))) * 100 if volume > 100: volume = 100 @@ -106,7 +106,7 @@ def calculate_v_receiving_dose(dose_grid, label, dose_threshold, relative=True): if relative: return relative_volume - total_volume = (mask_array > 0).sum() * np.product(label.GetSpacing()) / 1000 + total_volume = (mask_array > 0).sum() * np.prod(label.GetSpacing()) / 1000 return relative_volume * total_volume diff --git a/platipy/imaging/label/comparison.py b/platipy/imaging/label/comparison.py index 13572ecc..b59981fa 100644 --- a/platipy/imaging/label/comparison.py +++ b/platipy/imaging/label/comparison.py @@ -29,7 +29,7 @@ def compute_volume(label): float: The volume (in cubic centimetres) """ - return sitk.GetArrayFromImage(label).sum() * np.product(label.GetSpacing()) / 1000 + return sitk.GetArrayFromImage(label).sum() * np.prod(label.GetSpacing()) / 1000 def compute_surface_dsc(label_a, label_b, tau=3.0): @@ -159,7 +159,7 @@ def compute_volume_metrics(label_a, label_b): arr_intersection = arr_a & arr_b arr_union = arr_a | arr_b - voxel_volume = np.product(label_a.GetSpacing()) / 1000.0 # Conversion to cm^3 + voxel_volume = np.prod(label_a.GetSpacing()) / 1000.0 # Conversion to cm^3 # 2|A & B|/(|A|+|B|) dsc = (2.0 * arr_intersection.sum()) / (arr_a.sum() + arr_b.sum()) diff --git a/platipy/imaging/label/fusion.py b/platipy/imaging/label/fusion.py index de384750..f280d17a 100644 --- a/platipy/imaging/label/fusion.py +++ b/platipy/imaging/label/fusion.py @@ -109,7 +109,7 @@ def compute_weight_map( view_mask = view_as_windows(arr_mask, window_box_im) # Flatten to have a list of patches (that are also flattened) - new_shape = (np.product(view_target.shape[:3]), np.product(view_target.shape[3:])) + new_shape = (np.prod(view_target.shape[:3]), np.prod(view_target.shape[3:])) view_target_flat = np.reshape(view_target, new_shape) view_moving_flat = np.reshape(view_moving, new_shape) view_mask_flat = np.reshape(view_mask, new_shape) diff --git a/platipy/imaging/projects/cardiac/run.py b/platipy/imaging/projects/cardiac/run.py index 7d38b498..a20e24ad 100644 --- a/platipy/imaging/projects/cardiac/run.py +++ b/platipy/imaging/projects/cardiac/run.py @@ -567,7 +567,7 @@ def run_cardiac_segmentation(img, guide_structure=None, settings=CARDIAC_SETTING if crop_atlas_to_structures: logger.info("Automatically cropping atlas: %s", atlas_id) - original_volume = np.product(image.GetSize()) + original_volume = np.prod(image.GetSize()) crop_box_size, crop_box_index = label_to_roi( structures.values(), expansion_mm=crop_atlas_expansion_mm @@ -575,7 +575,7 @@ def run_cardiac_segmentation(img, guide_structure=None, settings=CARDIAC_SETTING image = crop_to_roi(image, size=crop_box_size, index=crop_box_index) - final_volume = np.product(image.GetSize()) + final_volume = np.prod(image.GetSize()) logger.info(" > Volume reduced by factor %.2f", original_volume / final_volume) @@ -654,7 +654,7 @@ def run_cardiac_segmentation(img, guide_structure=None, settings=CARDIAC_SETTING logger.info("Calculated crop box:") logger.info(" > %s", crop_box_index) logger.info(" > %s", crop_box_size) - logger.info(" > Vol reduction = %.2f", np.product(img.GetSize()) / np.product(crop_box_size)) + logger.info(" > Vol reduction = %.2f", np.prod(img.GetSize()) / np.prod(crop_box_size)) """ Step 2 - Rigid registration of target images diff --git a/platipy/imaging/projects/multiatlas/run.py b/platipy/imaging/projects/multiatlas/run.py index 7147c197..59f0cbc2 100644 --- a/platipy/imaging/projects/multiatlas/run.py +++ b/platipy/imaging/projects/multiatlas/run.py @@ -167,7 +167,7 @@ def run_segmentation(img, settings=MUTLIATLAS_SETTINGS_DEFAULTS): if crop_atlas_to_structures: logger.info("Automatically cropping atlas: %s", atlas_id) - original_volume = np.product(image.GetSize()) + original_volume = np.prod(image.GetSize()) crop_box_size, crop_box_index = label_to_roi( structures.values(), expansion_mm=crop_atlas_expansion_mm @@ -175,7 +175,7 @@ def run_segmentation(img, settings=MUTLIATLAS_SETTINGS_DEFAULTS): image = crop_to_roi(image, size=crop_box_size, index=crop_box_index) - final_volume = np.product(image.GetSize()) + final_volume = np.prod(image.GetSize()) logger.info(" > Volume reduced by factor %.2f", original_volume/final_volume) @@ -245,7 +245,7 @@ def run_segmentation(img, settings=MUTLIATLAS_SETTINGS_DEFAULTS): logger.info("Calculated crop box:") logger.info(" > %s", crop_box_index) logger.info(" > %s", crop_box_size) - logger.info(" > Vol reduction = %.2f", np.product(img.GetSize())/np.product(crop_box_size)) + logger.info(" > Vol reduction = %.2f", np.prod(img.GetSize())/np.prod(crop_box_size)) """ Step 2 - Rigid registration of target images diff --git a/platipy/imaging/utils/valve.py b/platipy/imaging/utils/valve.py index e95edab5..d2676c85 100644 --- a/platipy/imaging/utils/valve.py +++ b/platipy/imaging/utils/valve.py @@ -120,7 +120,7 @@ def generate_valve_using_cylinder( overlap = sitk.BinaryDilate(label_atrium, dilation_img) & sitk.BinaryDilate( label_ventricle, dilation_img ) - overlap_vol = np.sum(sitk.GetArrayFromImage(overlap) * np.product(overlap.GetSpacing())) + overlap_vol = np.sum(sitk.GetArrayFromImage(overlap) * np.prod(overlap.GetSpacing())) dilation += 1 # Now we can calculate the location of the valve diff --git a/platipy/imaging/utils/ventricle.py b/platipy/imaging/utils/ventricle.py index 799dc5c3..64551972 100644 --- a/platipy/imaging/utils/ventricle.py +++ b/platipy/imaging/utils/ventricle.py @@ -65,7 +65,7 @@ def extract( segment_img.CopyInformation(template_img) # Make sure area exceeds lower bound - area = segment_arr.sum() * np.product(segment_img.GetSpacing()) + area = segment_arr.sum() * np.prod(segment_img.GetSpacing()) if area < min_area_mm2: segment_img *= 0 @@ -167,8 +167,8 @@ def generate_left_ventricle_segments( if verbose: print("Module 1: Cropping and initial alignment.") - vol_before = np.product(contours[label_heart].GetSize()) - vol_after = np.product(working_contours[label_heart].GetSize()) + vol_before = np.prod(contours[label_heart].GetSize()) + vol_after = np.prod(working_contours[label_heart].GetSize()) print(f" Images cropped. Volume reduction: {vol_before/vol_after:.3f}") # Initially we should reorient based on the cardiac axis From dd058060cd7877ae7cc17da23fd3da26290d61dd Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 20 Jul 2023 12:09:52 +0000 Subject: [PATCH 07/32] Bump pygments from 2.14.0 to 2.15.0 Bumps [pygments](https://github.com/pygments/pygments) from 2.14.0 to 2.15.0. - [Release notes](https://github.com/pygments/pygments/releases) - [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES) - [Commits](https://github.com/pygments/pygments/compare/2.14.0...2.15.0) --- updated-dependencies: - dependency-name: pygments dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 224 +++------------------------------------------------- 1 file changed, 10 insertions(+), 214 deletions(-) diff --git a/poetry.lock b/poetry.lock index ea4e9a71..de67f1cf 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -16,7 +15,6 @@ files = [ name = "amqp" version = "5.1.1" description = "Low-level AMQP client for Python (fork of amqplib)." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -31,7 +29,6 @@ vine = ">=5.0.0" name = "aniso8601" version = "9.0.1" description = "A library for parsing ISO 8601 strings." -category = "main" optional = true python-versions = "*" files = [ @@ -46,7 +43,6 @@ dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] name = "anyio" version = "3.6.2" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "dev" optional = false python-versions = ">=3.6.2" files = [ @@ -67,7 +63,6 @@ trio = ["trio (>=0.16,<0.22)"] name = "appnope" version = "0.1.3" description = "Disable App Nap on macOS >= 10.9" -category = "main" optional = false python-versions = "*" files = [ @@ -79,7 +74,6 @@ files = [ name = "argh" version = "0.26.2" description = "An unobtrusive argparse wrapper with natural syntax" -category = "dev" optional = false python-versions = "*" files = [ @@ -91,7 +85,6 @@ files = [ name = "argon2-cffi" version = "21.3.0" description = "The secure Argon2 password hashing algorithm." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -111,7 +104,6 @@ tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"] name = "argon2-cffi-bindings" version = "21.2.0" description = "Low-level CFFI bindings for Argon2" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -149,7 +141,6 @@ tests = ["pytest"] name = "argparse" version = "1.4.0" description = "Python command-line parsing library" -category = "main" optional = true python-versions = "*" files = [ @@ -161,7 +152,6 @@ files = [ name = "arrow" version = "1.2.3" description = "Better dates & times for Python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -176,7 +166,6 @@ python-dateutil = ">=2.7.0" name = "astroid" version = "2.13.2" description = "An abstract syntax tree for Python with inference support." -category = "dev" optional = false python-versions = ">=3.7.2" files = [ @@ -196,7 +185,6 @@ wrapt = [ name = "asttokens" version = "2.2.1" description = "Annotate AST trees with source code positions" -category = "main" optional = false python-versions = "*" files = [ @@ -214,7 +202,6 @@ test = ["astroid", "pytest"] name = "async-timeout" version = "4.0.2" description = "Timeout context manager for asyncio programs" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -226,7 +213,6 @@ files = [ name = "atomicwrites" version = "1.4.1" description = "Atomic file writes." -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -237,7 +223,6 @@ files = [ name = "attrs" version = "22.2.0" description = "Classes Without Boilerplate" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -256,7 +241,6 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy name = "babel" version = "2.11.0" description = "Internationalization utilities" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -271,7 +255,6 @@ pytz = ">=2015.7" name = "backcall" version = "0.2.0" description = "Specifications for callback functions passed in to an API" -category = "main" optional = false python-versions = "*" files = [ @@ -283,7 +266,6 @@ files = [ name = "batchgenerators" version = "0.24" description = "Data augmentation toolkit" -category = "main" optional = true python-versions = "*" files = [ @@ -304,7 +286,6 @@ unittest2 = "*" name = "beautifulsoup4" version = "4.11.1" description = "Screen-scraping library" -category = "dev" optional = false python-versions = ">=3.6.0" files = [ @@ -323,7 +304,6 @@ lxml = ["lxml"] name = "billiard" version = "3.6.4.0" description = "Python multiprocessing fork with improvements and bugfixes" -category = "main" optional = true python-versions = "*" files = [ @@ -335,7 +315,6 @@ files = [ name = "black" version = "22.12.0" description = "The uncompromising code formatter." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -371,7 +350,6 @@ uvloop = ["uvloop (>=0.15.2)"] name = "bleach" version = "5.0.1" description = "An easy safelist-based HTML-sanitizing tool." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -391,7 +369,6 @@ dev = ["Sphinx (==4.3.2)", "black (==22.3.0)", "build (==0.8.0)", "flake8 (==4.0 name = "blinker" version = "1.6.2" description = "Fast, simple object-to-object and broadcast signaling" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -403,7 +380,6 @@ files = [ name = "celery" version = "5.2.7" description = "Distributed Task Queue." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -458,7 +434,6 @@ zstd = ["zstandard"] name = "certifi" version = "2022.12.7" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -470,7 +445,6 @@ files = [ name = "cffi" version = "1.15.1" description = "Foreign Function Interface for Python calling C code." -category = "dev" optional = false python-versions = "*" files = [ @@ -547,7 +521,6 @@ pycparser = "*" name = "charset-normalizer" version = "3.0.1" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = "*" files = [ @@ -645,7 +618,6 @@ files = [ name = "click" version = "8.1.3" description = "Composable command line interface toolkit" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -660,7 +632,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "click-didyoumean" version = "0.3.0" description = "Enables git-like *did-you-mean* feature in click" -category = "main" optional = true python-versions = ">=3.6.2,<4.0.0" files = [ @@ -675,7 +646,6 @@ click = ">=7" name = "click-plugins" version = "1.1.1" description = "An extension module for click to enable registering CLI commands via setuptools entry-points." -category = "main" optional = true python-versions = "*" files = [ @@ -693,7 +663,6 @@ dev = ["coveralls", "pytest (>=3.6)", "pytest-cov", "wheel"] name = "click-repl" version = "0.2.0" description = "REPL plugin for Click" -category = "main" optional = true python-versions = "*" files = [ @@ -710,7 +679,6 @@ six = "*" name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -722,7 +690,6 @@ files = [ name = "comm" version = "0.1.2" description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -740,7 +707,6 @@ test = ["pytest"] name = "contourpy" version = "1.0.7" description = "Python library for calculating contours of 2D quadrilateral grids" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -815,7 +781,6 @@ test-no-images = ["pytest"] name = "cycler" version = "0.11.0" description = "Composable style cycles" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -827,7 +792,6 @@ files = [ name = "dataclasses" version = "0.6" description = "A backport of the dataclasses module for Python 3.6" -category = "main" optional = false python-versions = "*" files = [ @@ -839,7 +803,6 @@ files = [ name = "debugpy" version = "1.6.5" description = "An implementation of the Debug Adapter Protocol for Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -867,7 +830,6 @@ files = [ name = "decorator" version = "5.1.1" description = "Decorators for Humans" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -879,7 +841,6 @@ files = [ name = "defusedxml" version = "0.7.1" description = "XML bomb protection for Python stdlib modules" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -891,7 +852,6 @@ files = [ name = "dicom2nifti" version = "2.4.7" description = "package for converting dicom files to nifti" -category = "main" optional = true python-versions = "*" files = [ @@ -910,7 +870,6 @@ scipy = "*" name = "dill" version = "0.3.6" description = "serialize all of python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -925,7 +884,6 @@ graph = ["objgraph (>=1.7.2)"] name = "docutils" version = "0.19" description = "Docutils -- Python Documentation Utilities" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -937,7 +895,6 @@ files = [ name = "entrypoints" version = "0.4" description = "Discover and load entry points from installed packages." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -949,7 +906,6 @@ files = [ name = "executing" version = "1.2.0" description = "Get the currently executing AST node of a frame, and other information" -category = "main" optional = false python-versions = "*" files = [ @@ -964,7 +920,6 @@ tests = ["asttokens", "littleutils", "pytest", "rich"] name = "fastjsonschema" version = "2.16.2" description = "Fastest Python implementation of JSON schema" -category = "dev" optional = false python-versions = "*" files = [ @@ -979,7 +934,6 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc name = "flask" version = "2.3.2" description = "A simple framework for building complex web applications." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1003,7 +957,6 @@ dotenv = ["python-dotenv"] name = "flask-restful" version = "0.3.9" description = "Simple framework for creating REST APIs" -category = "main" optional = true python-versions = "*" files = [ @@ -1024,7 +977,6 @@ docs = ["sphinx"] name = "flask-sqlalchemy" version = "2.5.1" description = "Adds SQLAlchemy support to your Flask application." -category = "main" optional = false python-versions = ">= 2.7, != 3.0.*, != 3.1.*, != 3.2.*, != 3.3.*" files = [ @@ -1040,7 +992,6 @@ SQLAlchemy = ">=0.8.0" name = "fonttools" version = "4.38.0" description = "Tools to manipulate font files" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1066,7 +1017,6 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] name = "fqdn" version = "1.5.1" description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" -category = "dev" optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" files = [ @@ -1078,7 +1028,6 @@ files = [ name = "furo" version = "2022.12.7" description = "A clean customisable Sphinx documentation theme." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1096,7 +1045,6 @@ sphinx-basic-ng = "*" name = "future" version = "0.18.3" description = "Clean single-source support for Python 3 and 2" -category = "main" optional = true python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1107,7 +1055,6 @@ files = [ name = "greenlet" version = "2.0.1" description = "Lightweight in-process concurrent programming" -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" files = [ @@ -1181,7 +1128,6 @@ test = ["faulthandler", "objgraph", "psutil"] name = "gunicorn" version = "20.1.0" description = "WSGI HTTP Server for UNIX" -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -1202,7 +1148,6 @@ tornado = ["tornado (>=0.2)"] name = "idna" version = "3.4" description = "Internationalized Domain Names in Applications (IDNA)" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -1214,7 +1159,6 @@ files = [ name = "imageio" version = "2.24.0" description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1247,7 +1191,6 @@ tifffile = ["tifffile"] name = "imagesize" version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1259,7 +1202,6 @@ files = [ name = "importlib-metadata" version = "6.0.0" description = "Read metadata from Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1279,7 +1221,6 @@ testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packag name = "importlib-resources" version = "5.10.2" description = "Read resources from Python packages" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1298,7 +1239,6 @@ testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-chec name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1310,7 +1250,6 @@ files = [ name = "ipykernel" version = "6.20.2" description = "IPython Kernel for Jupyter" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1343,7 +1282,6 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio" name = "ipython" version = "8.10.0" description = "IPython: Productive Interactive Computing" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1382,7 +1320,6 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pa name = "ipython-genutils" version = "0.2.0" description = "Vestigial utilities from IPython" -category = "dev" optional = false python-versions = "*" files = [ @@ -1394,7 +1331,6 @@ files = [ name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1409,7 +1345,6 @@ arrow = ">=0.15.0" name = "isort" version = "5.11.4" description = "A Python utility / library to sort Python imports." -category = "dev" optional = false python-versions = ">=3.7.0" files = [ @@ -1427,7 +1362,6 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] name = "itsdangerous" version = "2.1.2" description = "Safely pass data to untrusted environments and back." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1439,7 +1373,6 @@ files = [ name = "jedi" version = "0.18.2" description = "An autocompletion tool for Python that can be used for text editors." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1459,7 +1392,6 @@ testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] name = "jinja2" version = "3.1.2" description = "A very fast and expressive template engine." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1477,7 +1409,6 @@ i18n = ["Babel (>=2.7)"] name = "joblib" version = "1.2.0" description = "Lightweight pipelining with Python functions" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1489,7 +1420,6 @@ files = [ name = "json5" version = "0.9.11" description = "A Python implementation of the JSON5 data format." -category = "dev" optional = false python-versions = "*" files = [ @@ -1504,7 +1434,6 @@ dev = ["hypothesis"] name = "jsonpointer" version = "2.3" description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1516,7 +1445,6 @@ files = [ name = "jsonschema" version = "4.17.3" description = "An implementation of JSON Schema validation for Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1546,7 +1474,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jupyter-client" version = "7.4.9" description = "Jupyter protocol implementation and client libraries" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1571,7 +1498,6 @@ test = ["codecov", "coverage", "ipykernel (>=6.12)", "ipython", "mypy", "pre-com name = "jupyter-core" version = "5.1.3" description = "Jupyter core package. A base package on which Jupyter projects rely." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1592,7 +1518,6 @@ test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] name = "jupyter-events" version = "0.6.3" description = "Jupyter Event System library" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1617,7 +1542,6 @@ test = ["click", "coverage", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>= name = "jupyter-server" version = "2.1.0" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1630,7 +1554,7 @@ anyio = ">=3.1.0,<4" argon2-cffi = "*" jinja2 = "*" jupyter-client = ">=7.4.4" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" jupyter-events = ">=0.4.0" jupyter-server-terminals = "*" nbconvert = ">=6.4.4" @@ -1653,7 +1577,6 @@ test = ["ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", " name = "jupyter-server-terminals" version = "0.4.4" description = "A Jupyter Server Extension Providing Terminals." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1673,7 +1596,6 @@ test = ["coverage", "jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-cov", name = "jupyterlab" version = "3.5.2" description = "JupyterLab computational environment" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1700,7 +1622,6 @@ test = ["check-manifest", "coverage", "jupyterlab-server[test]", "pre-commit", " name = "jupyterlab-pygments" version = "0.2.2" description = "Pygments theme using JupyterLab CSS variables" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1712,7 +1633,6 @@ files = [ name = "jupyterlab-server" version = "2.19.0" description = "A set of server components for JupyterLab and JupyterLab like applications." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1739,7 +1659,6 @@ test = ["codecov", "ipykernel", "jupyterlab-server[openapi]", "openapi-spec-vali name = "kiwisolver" version = "1.4.4" description = "A fast implementation of the Cassowary constraint solver" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1817,7 +1736,6 @@ files = [ name = "kombu" version = "5.2.4" description = "Messaging library for Python." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1849,7 +1767,6 @@ zookeeper = ["kazoo (>=1.3.1)"] name = "lazy-object-proxy" version = "1.9.0" description = "A fast and thorough lazy object proxy." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1895,7 +1812,6 @@ files = [ name = "linecache2" version = "1.0.0" description = "Backports of the linecache module" -category = "main" optional = true python-versions = "*" files = [ @@ -1907,7 +1823,6 @@ files = [ name = "lxml" version = "4.9.2" description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*" files = [ @@ -2000,7 +1915,6 @@ source = ["Cython (>=0.29.7)"] name = "m2r2" version = "0.3.3" description = "Markdown and reStructuredText in a single file." -category = "dev" optional = false python-versions = "*" files = [ @@ -2016,7 +1930,6 @@ mistune = "0.8.4" name = "markupsafe" version = "2.1.1" description = "Safely add untrusted strings to HTML/XML markup." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2066,7 +1979,6 @@ files = [ name = "matplotlib" version = "3.6.3" description = "Python plotting package" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2128,7 +2040,6 @@ python-dateutil = ">=2.7" name = "matplotlib-inline" version = "0.1.6" description = "Inline Matplotlib backend for Jupyter" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -2143,7 +2054,6 @@ traitlets = "*" name = "mccabe" version = "0.7.0" description = "McCabe checker, plugin for flake8" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2155,7 +2065,6 @@ files = [ name = "medpy" version = "0.4.0" description = "Medical image processing in Python" -category = "main" optional = true python-versions = "*" files = [ @@ -2171,7 +2080,6 @@ SimpleITK = ">=1.1.0" name = "mistune" version = "0.8.4" description = "The fastest markdown parser in pure Python" -category = "dev" optional = false python-versions = "*" files = [ @@ -2183,7 +2091,6 @@ files = [ name = "mypy-extensions" version = "0.4.3" description = "Experimental type system extensions for programs checked with the mypy typechecker." -category = "dev" optional = false python-versions = "*" files = [ @@ -2195,7 +2102,6 @@ files = [ name = "nbclassic" version = "0.4.8" description = "A web-based notebook environment for interactive computing" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2231,7 +2137,6 @@ test = ["coverage", "nbval", "pytest", "pytest-cov", "pytest-playwright", "pytes name = "nbclient" version = "0.7.2" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." -category = "dev" optional = false python-versions = ">=3.7.0" files = [ @@ -2241,7 +2146,7 @@ files = [ [package.dependencies] jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" nbformat = ">=5.1" traitlets = ">=5.3" @@ -2254,7 +2159,6 @@ test = ["ipykernel", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>= name = "nbconvert" version = "6.5.4" description = "Converting Jupyter Notebooks" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2292,7 +2196,6 @@ webpdf = ["pyppeteer (>=1,<1.1)"] name = "nbformat" version = "5.7.3" description = "The Jupyter Notebook format" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2314,7 +2217,6 @@ test = ["pep440", "pre-commit", "pytest", "testpath"] name = "nbsphinx" version = "0.8.11" description = "Jupyter Notebook Tools for Sphinx" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2334,7 +2236,6 @@ traitlets = ">=5" name = "nbstripout" version = "0.3.9" description = "Strips outputs from Jupyter and IPython notebooks" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2349,7 +2250,6 @@ nbformat = "*" name = "nest-asyncio" version = "1.5.6" description = "Patch asyncio to allow nested event loops" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2361,7 +2261,6 @@ files = [ name = "networkx" version = "3.0" description = "Python package for creating and manipulating graphs and networks" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2380,7 +2279,6 @@ test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"] name = "nibabel" version = "5.0.0" description = "Access a multitude of neuroimaging data formats" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -2411,7 +2309,6 @@ zstd = ["pyzstd (>=0.14.3)"] name = "nnunet" version = "1.7.0" description = "nnU-Net. Framework for out-of-the box biomedical image segmentation." -category = "main" optional = true python-versions = "*" files = [ @@ -2438,7 +2335,6 @@ tqdm = "*" name = "notebook" version = "6.5.2" description = "A web-based notebook environment for interactive computing" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2473,7 +2369,6 @@ test = ["coverage", "nbval", "pytest", "pytest-cov", "requests", "requests-unixs name = "notebook-shim" version = "0.2.2" description = "A shim layer for notebook traits and config" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2491,7 +2386,6 @@ test = ["pytest", "pytest-console-scripts", "pytest-tornasync"] name = "numpy" version = "1.24.1" description = "Fundamental package for array computing in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2529,7 +2423,6 @@ files = [ name = "nvidia-cublas-cu11" version = "11.10.3.66" description = "CUBLAS native runtime libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -2545,7 +2438,6 @@ wheel = "*" name = "nvidia-cuda-nvrtc-cu11" version = "11.7.99" description = "NVRTC native runtime libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -2562,7 +2454,6 @@ wheel = "*" name = "nvidia-cuda-runtime-cu11" version = "11.7.99" description = "CUDA Runtime native Libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -2578,7 +2469,6 @@ wheel = "*" name = "nvidia-cudnn-cu11" version = "8.5.0.96" description = "cuDNN runtime libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -2594,7 +2484,6 @@ wheel = "*" name = "opencv-python" version = "4.7.0.68" description = "Wrapper package for OpenCV python bindings." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2621,7 +2510,6 @@ numpy = [ name = "packaging" version = "23.0" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2633,7 +2521,6 @@ files = [ name = "pandas" version = "1.5.2" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2682,7 +2569,6 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] name = "pandocfilters" version = "1.5.0" description = "Utilities for writing pandoc filters in python" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -2694,7 +2580,6 @@ files = [ name = "parso" version = "0.8.3" description = "A Python Parser" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2710,7 +2595,6 @@ testing = ["docopt", "pytest (<6.0.0)"] name = "pathspec" version = "0.10.3" description = "Utility library for gitignore style pattern matching of file paths." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2722,7 +2606,6 @@ files = [ name = "pexpect" version = "4.8.0" description = "Pexpect allows easy control of interactive console applications." -category = "main" optional = false python-versions = "*" files = [ @@ -2737,7 +2620,6 @@ ptyprocess = ">=0.5" name = "pickleshare" version = "0.7.5" description = "Tiny 'shelve'-like database with concurrency support" -category = "main" optional = false python-versions = "*" files = [ @@ -2749,7 +2631,6 @@ files = [ name = "pillow" version = "9.4.0" description = "Python Imaging Library (Fork)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2840,7 +2721,6 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa name = "pkgutil-resolve-name" version = "1.3.10" description = "Resolve a name to an object." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2852,7 +2732,6 @@ files = [ name = "platformdirs" version = "2.6.2" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2868,7 +2747,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2)", "pytest- name = "pluggy" version = "1.0.0" description = "plugin and hook calling mechanisms for python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2884,7 +2762,6 @@ testing = ["pytest", "pytest-benchmark"] name = "pockets" version = "0.9.1" description = "A collection of helpful Python tools!" -category = "dev" optional = false python-versions = "*" files = [ @@ -2899,7 +2776,6 @@ six = ">=1.5.2" name = "prometheus-client" version = "0.15.0" description = "Python client for the Prometheus monitoring system." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2914,7 +2790,6 @@ twisted = ["twisted"] name = "prompt-toolkit" version = "3.0.36" description = "Library for building powerful interactive command lines in Python" -category = "main" optional = false python-versions = ">=3.6.2" files = [ @@ -2929,7 +2804,6 @@ wcwidth = "*" name = "psutil" version = "5.9.4" description = "Cross-platform lib for process and system monitoring in Python." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -2956,7 +2830,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "ptyprocess" version = "0.7.0" description = "Run a subprocess in a pseudo terminal" -category = "main" optional = false python-versions = "*" files = [ @@ -2968,7 +2841,6 @@ files = [ name = "pure-eval" version = "0.2.2" description = "Safely evaluate AST nodes without side effects" -category = "main" optional = false python-versions = "*" files = [ @@ -2983,7 +2855,6 @@ tests = ["pytest"] name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2995,7 +2866,6 @@ files = [ name = "pycparser" version = "2.21" description = "C parser in Python" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3007,7 +2877,6 @@ files = [ name = "pydicom" version = "2.3.1" description = "A pure Python package for reading and writing DICOM data" -category = "main" optional = false python-versions = ">=3.6.1" files = [ @@ -3020,14 +2889,13 @@ docs = ["matplotlib", "numpy", "numpydoc", "pillow", "sphinx", "sphinx-copybutto [[package]] name = "pygments" -version = "2.14.0" +version = "2.15.0" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "Pygments-2.14.0-py3-none-any.whl", hash = "sha256:fa7bd7bd2771287c0de303af8bfdfc731f51bd2c6a47ab69d117138893b82717"}, - {file = "Pygments-2.14.0.tar.gz", hash = "sha256:b3ed06a9e8ac9a9aae5a6f5dbe78a8a58655d17b43b93c078f094ddc476ae297"}, + {file = "Pygments-2.15.0-py3-none-any.whl", hash = "sha256:77a3299119af881904cd5ecd1ac6a66214b6e9bed1f2db16993b54adede64094"}, + {file = "Pygments-2.15.0.tar.gz", hash = "sha256:f7e36cffc4c517fbc252861b9a6e4644ca0e5abadf9a113c72d1358ad09b9500"}, ] [package.extras] @@ -3037,7 +2905,6 @@ plugins = ["importlib-metadata"] name = "pylint" version = "2.15.10" description = "python code static checker" -category = "dev" optional = false python-versions = ">=3.7.2" files = [ @@ -3067,7 +2934,6 @@ testutils = ["gitpython (>3)"] name = "pylint-flask-sqlalchemy" version = "0.2.0" description = "A Pylint plugin for improving code analysis when editing code using Flask-SQLAlchemy" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -3086,7 +2952,6 @@ dev = ["black", "bump2version", "gitchangelog", "mypy", "pystache"] name = "pymedphys" version = "0.38.0" description = "Medical Physics library" -category = "main" optional = true python-versions = ">=3.7,<4.0" files = [ @@ -3115,7 +2980,6 @@ user = ["Pillow (>=9.0.0)", "PyYAML", "attrs", "dbfread", "dicompyler-core", "fs name = "pynetdicom" version = "2.0.2" description = "A Python implementation of the DICOM networking protocol" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3135,7 +2999,6 @@ tests = ["pyfakefs", "pytest", "sqlalchemy"] name = "pyparsing" version = "3.0.9" description = "pyparsing module - Classes and methods to define and execute parsing grammars" -category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -3150,7 +3013,6 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pyrsistent" version = "0.19.3" description = "Persistent/Functional/Immutable data structures" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3187,7 +3049,6 @@ files = [ name = "pytest" version = "6.2.5" description = "pytest: simple powerful testing with Python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3212,7 +3073,6 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -3227,7 +3087,6 @@ six = ">=1.5" name = "python-gdcm" version = "3.0.20" description = "Grassroots DICOM runtime libraries" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -3278,7 +3137,6 @@ files = [ name = "python-json-logger" version = "2.0.4" description = "A python library adding a json log formatter" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -3290,7 +3148,6 @@ files = [ name = "pytz" version = "2022.7.1" description = "World timezone definitions, modern and historical" -category = "main" optional = false python-versions = "*" files = [ @@ -3302,7 +3159,6 @@ files = [ name = "pywavelets" version = "1.4.1" description = "PyWavelets, wavelet transform module" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3340,7 +3196,6 @@ numpy = ">=1.17.3" name = "pywin32" version = "305" description = "Python for Window Extensions" -category = "dev" optional = false python-versions = "*" files = [ @@ -3364,7 +3219,6 @@ files = [ name = "pywinpty" version = "2.0.10" description = "Pseudo terminal support for Windows from Python." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3380,7 +3234,6 @@ files = [ name = "pyyaml" version = "6.0" description = "YAML parser and emitter for Python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3430,7 +3283,6 @@ files = [ name = "pyzmq" version = "25.0.0" description = "Python bindings for 0MQ" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3520,7 +3372,6 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""} name = "redis" version = "4.5.4" description = "Python client for Redis database and key-value store" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3539,7 +3390,6 @@ ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)" name = "requests" version = "2.28.2" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7, <4" files = [ @@ -3561,7 +3411,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "rfc3339-validator" version = "0.1.4" description = "A pure python RFC3339 validator" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3576,7 +3425,6 @@ six = "*" name = "rfc3986-validator" version = "0.1.1" description = "Pure python rfc3986 validator" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3588,7 +3436,6 @@ files = [ name = "rt-utils" version = "1.2.7" description = "A small library for handling masks and RT-Structs" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3606,7 +3453,6 @@ pydicom = "*" name = "scikit-image" version = "0.19.3" description = "Image processing in Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3658,7 +3504,6 @@ test = ["asv", "codecov", "flake8", "matplotlib (>=3.0.3)", "pooch (>=1.3.0)", " name = "scikit-learn" version = "1.2.0" description = "A set of python modules for machine learning and data mining" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -3701,7 +3546,6 @@ tests = ["black (>=22.3.0)", "flake8 (>=3.8.2)", "matplotlib (>=3.1.3)", "mypy ( name = "scipy" version = "1.9.3" description = "Fundamental algorithms for scientific computing in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3740,7 +3584,6 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki name = "send2trash" version = "1.8.0" description = "Send file to trash natively under Mac OS X, Windows and Linux." -category = "dev" optional = false python-versions = "*" files = [ @@ -3757,7 +3600,6 @@ win32 = ["pywin32"] name = "setuptools" version = "66.0.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3774,7 +3616,6 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs ( name = "simpleitk" version = "2.2.1" description = "SimpleITK is a simplified interface to the Insight Toolkit (ITK) for image registration and segmentation" -category = "main" optional = false python-versions = "*" files = [ @@ -3808,7 +3649,6 @@ files = [ name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3820,7 +3660,6 @@ files = [ name = "sklearn" version = "0.0.post1" description = "deprecated sklearn package, use scikit-learn instead" -category = "main" optional = true python-versions = "*" files = [ @@ -3831,7 +3670,6 @@ files = [ name = "sniffio" version = "1.3.0" description = "Sniff out which async library your code is running under" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3843,7 +3681,6 @@ files = [ name = "snowballstemmer" version = "2.2.0" description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." -category = "dev" optional = false python-versions = "*" files = [ @@ -3855,7 +3692,6 @@ files = [ name = "soupsieve" version = "2.3.2.post1" description = "A modern CSS selector implementation for Beautiful Soup." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3867,7 +3703,6 @@ files = [ name = "sphinx" version = "5.3.0" description = "Python documentation generator" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3903,7 +3738,6 @@ test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"] name = "sphinx-basic-ng" version = "1.0.0b1" description = "A modern skeleton for Sphinx themes." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3921,7 +3755,6 @@ docs = ["furo", "ipython", "myst-parser", "sphinx-copybutton", "sphinx-inline-ta name = "sphinx-click" version = "4.4.0" description = "Sphinx extension that automatically documents click applications" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3938,7 +3771,6 @@ sphinx = ">=2.0" name = "sphinx-theme" version = "1.0" description = "Sphinx documentation theme based on readthedocs.org" -category = "dev" optional = false python-versions = "*" files = [ @@ -3950,7 +3782,6 @@ files = [ name = "sphinxcontrib-applehelp" version = "1.0.3" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3966,7 +3797,6 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.2" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -3982,7 +3812,6 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.0" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3998,7 +3827,6 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -4013,7 +3841,6 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-napoleon" version = "0.7" description = "Sphinx \"napoleon\" extension." -category = "dev" optional = false python-versions = "*" files = [ @@ -4029,7 +3856,6 @@ six = ">=1.5.2" name = "sphinxcontrib-qthelp" version = "1.0.3" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -4045,7 +3871,6 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -4061,7 +3886,6 @@ test = ["pytest"] name = "sqlalchemy" version = "1.4.46" description = "Database Abstraction Library" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -4109,7 +3933,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\")"} [package.extras] aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] @@ -4136,7 +3960,6 @@ sqlcipher = ["sqlcipher3-binary"] name = "stack-data" version = "0.6.2" description = "Extract data from python stack frames and tracebacks for informative displays" -category = "main" optional = false python-versions = "*" files = [ @@ -4156,7 +3979,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] name = "terminado" version = "0.17.1" description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4177,7 +3999,6 @@ test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"] name = "threadpoolctl" version = "3.1.0" description = "threadpoolctl" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -4189,7 +4010,6 @@ files = [ name = "tifffile" version = "2022.10.10" description = "Read and write TIFF files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4207,7 +4027,6 @@ all = ["fsspec", "imagecodecs (>=2022.2.22)", "lxml", "matplotlib (>=3.3)", "zar name = "tinycss2" version = "1.2.1" description = "A tiny CSS parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4226,7 +4045,6 @@ test = ["flake8", "isort", "pytest"] name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" -category = "dev" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -4238,7 +4056,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4250,7 +4067,6 @@ files = [ name = "tomlkit" version = "0.11.6" description = "Style preserving TOML library" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4262,7 +4078,6 @@ files = [ name = "torch" version = "1.13.1" description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration" -category = "main" optional = true python-versions = ">=3.7.0" files = [ @@ -4303,7 +4118,6 @@ opt-einsum = ["opt-einsum (>=3.3)"] name = "tornado" version = "6.3.2" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." -category = "dev" optional = false python-versions = ">= 3.8" files = [ @@ -4324,7 +4138,6 @@ files = [ name = "tqdm" version = "4.64.1" description = "Fast, Extensible Progress Meter" -category = "main" optional = true python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" files = [ @@ -4345,7 +4158,6 @@ telegram = ["requests"] name = "traceback2" version = "1.4.0" description = "Backports of the traceback module" -category = "main" optional = true python-versions = "*" files = [ @@ -4360,7 +4172,6 @@ linecache2 = "*" name = "traitlets" version = "5.8.1" description = "Traitlets Python configuration system" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4376,7 +4187,6 @@ test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] name = "typing-extensions" version = "4.4.0" description = "Backported and Experimental Type Hints for Python 3.7+" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4388,7 +4198,6 @@ files = [ name = "unittest2" version = "1.1.0" description = "The new features in unittest backported to Python 2.4+." -category = "main" optional = true python-versions = "*" files = [ @@ -4405,7 +4214,6 @@ traceback2 = "*" name = "uri-template" version = "1.2.0" description = "RFC 6570 URI Template Processor" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4420,7 +4228,6 @@ dev = ["flake8 (<4.0.0)", "flake8-annotations", "flake8-bugbear", "flake8-commas name = "urllib3" version = "1.26.14" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -4437,7 +4244,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "vine" version = "5.0.0" description = "Promises, promises, promises." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -4449,7 +4255,6 @@ files = [ name = "vtk" version = "9.2.5" description = "VTK is an open-source toolkit for 3D computer graphics, image processing, and visualization" -category = "main" optional = true python-versions = "*" files = [ @@ -4487,7 +4292,6 @@ web = ["wslink (>=1.0.4)"] name = "watchdog" version = "2.2.1" description = "Filesystem events monitoring" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4528,7 +4332,6 @@ watchmedo = ["PyYAML (>=3.10)"] name = "wcwidth" version = "0.2.6" description = "Measures the displayed width of unicode strings in a terminal" -category = "main" optional = false python-versions = "*" files = [ @@ -4540,7 +4343,6 @@ files = [ name = "webcolors" version = "1.12" description = "A library for working with color names and color values formats defined by HTML and CSS." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4552,7 +4354,6 @@ files = [ name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "dev" optional = false python-versions = "*" files = [ @@ -4564,7 +4365,6 @@ files = [ name = "websocket-client" version = "1.4.2" description = "WebSocket client for Python with low level API options" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4581,7 +4381,6 @@ test = ["websockets"] name = "werkzeug" version = "2.3.3" description = "The comprehensive WSGI web application library." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4599,7 +4398,6 @@ watchdog = ["watchdog (>=2.3)"] name = "wheel" version = "0.38.4" description = "A built-package format for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -4614,7 +4412,6 @@ test = ["pytest (>=3.0.0)"] name = "wrapt" version = "1.14.1" description = "Module for decorators, wrappers and monkey patching." -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -4688,7 +4485,6 @@ files = [ name = "zipp" version = "3.11.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4701,8 +4497,8 @@ docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [extras] -backend = ["Flask", "Flask-RESTful", "Flask-SQLAlchemy", "celery", "redis", "psutil", "gunicorn", "Jinja2", "pymedphys"] -cardiac = ["vtk", "nnunet"] +backend = ["Flask", "Flask-RESTful", "Flask-SQLAlchemy", "Jinja2", "celery", "gunicorn", "psutil", "pymedphys", "redis"] +cardiac = ["nnunet", "vtk"] nnunet = ["nnunet"] [metadata] From 00184fdac776b5e21fefe3378ee0eb2f66f359e1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 25 Jul 2023 21:10:23 +0000 Subject: [PATCH 08/32] Bump certifi from 2022.12.7 to 2023.7.22 Bumps [certifi](https://github.com/certifi/python-certifi) from 2022.12.7 to 2023.7.22. - [Commits](https://github.com/certifi/python-certifi/compare/2022.12.07...2023.07.22) --- updated-dependencies: - dependency-name: certifi dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 222 +++------------------------------------------------- 1 file changed, 9 insertions(+), 213 deletions(-) diff --git a/poetry.lock b/poetry.lock index ea4e9a71..94b399de 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -16,7 +15,6 @@ files = [ name = "amqp" version = "5.1.1" description = "Low-level AMQP client for Python (fork of amqplib)." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -31,7 +29,6 @@ vine = ">=5.0.0" name = "aniso8601" version = "9.0.1" description = "A library for parsing ISO 8601 strings." -category = "main" optional = true python-versions = "*" files = [ @@ -46,7 +43,6 @@ dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] name = "anyio" version = "3.6.2" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "dev" optional = false python-versions = ">=3.6.2" files = [ @@ -67,7 +63,6 @@ trio = ["trio (>=0.16,<0.22)"] name = "appnope" version = "0.1.3" description = "Disable App Nap on macOS >= 10.9" -category = "main" optional = false python-versions = "*" files = [ @@ -79,7 +74,6 @@ files = [ name = "argh" version = "0.26.2" description = "An unobtrusive argparse wrapper with natural syntax" -category = "dev" optional = false python-versions = "*" files = [ @@ -91,7 +85,6 @@ files = [ name = "argon2-cffi" version = "21.3.0" description = "The secure Argon2 password hashing algorithm." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -111,7 +104,6 @@ tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"] name = "argon2-cffi-bindings" version = "21.2.0" description = "Low-level CFFI bindings for Argon2" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -149,7 +141,6 @@ tests = ["pytest"] name = "argparse" version = "1.4.0" description = "Python command-line parsing library" -category = "main" optional = true python-versions = "*" files = [ @@ -161,7 +152,6 @@ files = [ name = "arrow" version = "1.2.3" description = "Better dates & times for Python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -176,7 +166,6 @@ python-dateutil = ">=2.7.0" name = "astroid" version = "2.13.2" description = "An abstract syntax tree for Python with inference support." -category = "dev" optional = false python-versions = ">=3.7.2" files = [ @@ -196,7 +185,6 @@ wrapt = [ name = "asttokens" version = "2.2.1" description = "Annotate AST trees with source code positions" -category = "main" optional = false python-versions = "*" files = [ @@ -214,7 +202,6 @@ test = ["astroid", "pytest"] name = "async-timeout" version = "4.0.2" description = "Timeout context manager for asyncio programs" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -226,7 +213,6 @@ files = [ name = "atomicwrites" version = "1.4.1" description = "Atomic file writes." -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -237,7 +223,6 @@ files = [ name = "attrs" version = "22.2.0" description = "Classes Without Boilerplate" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -256,7 +241,6 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy name = "babel" version = "2.11.0" description = "Internationalization utilities" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -271,7 +255,6 @@ pytz = ">=2015.7" name = "backcall" version = "0.2.0" description = "Specifications for callback functions passed in to an API" -category = "main" optional = false python-versions = "*" files = [ @@ -283,7 +266,6 @@ files = [ name = "batchgenerators" version = "0.24" description = "Data augmentation toolkit" -category = "main" optional = true python-versions = "*" files = [ @@ -304,7 +286,6 @@ unittest2 = "*" name = "beautifulsoup4" version = "4.11.1" description = "Screen-scraping library" -category = "dev" optional = false python-versions = ">=3.6.0" files = [ @@ -323,7 +304,6 @@ lxml = ["lxml"] name = "billiard" version = "3.6.4.0" description = "Python multiprocessing fork with improvements and bugfixes" -category = "main" optional = true python-versions = "*" files = [ @@ -335,7 +315,6 @@ files = [ name = "black" version = "22.12.0" description = "The uncompromising code formatter." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -371,7 +350,6 @@ uvloop = ["uvloop (>=0.15.2)"] name = "bleach" version = "5.0.1" description = "An easy safelist-based HTML-sanitizing tool." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -391,7 +369,6 @@ dev = ["Sphinx (==4.3.2)", "black (==22.3.0)", "build (==0.8.0)", "flake8 (==4.0 name = "blinker" version = "1.6.2" description = "Fast, simple object-to-object and broadcast signaling" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -403,7 +380,6 @@ files = [ name = "celery" version = "5.2.7" description = "Distributed Task Queue." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -456,21 +432,19 @@ zstd = ["zstandard"] [[package]] name = "certifi" -version = "2022.12.7" +version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"}, - {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"}, + {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, + {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, ] [[package]] name = "cffi" version = "1.15.1" description = "Foreign Function Interface for Python calling C code." -category = "dev" optional = false python-versions = "*" files = [ @@ -547,7 +521,6 @@ pycparser = "*" name = "charset-normalizer" version = "3.0.1" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = "*" files = [ @@ -645,7 +618,6 @@ files = [ name = "click" version = "8.1.3" description = "Composable command line interface toolkit" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -660,7 +632,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "click-didyoumean" version = "0.3.0" description = "Enables git-like *did-you-mean* feature in click" -category = "main" optional = true python-versions = ">=3.6.2,<4.0.0" files = [ @@ -675,7 +646,6 @@ click = ">=7" name = "click-plugins" version = "1.1.1" description = "An extension module for click to enable registering CLI commands via setuptools entry-points." -category = "main" optional = true python-versions = "*" files = [ @@ -693,7 +663,6 @@ dev = ["coveralls", "pytest (>=3.6)", "pytest-cov", "wheel"] name = "click-repl" version = "0.2.0" description = "REPL plugin for Click" -category = "main" optional = true python-versions = "*" files = [ @@ -710,7 +679,6 @@ six = "*" name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -722,7 +690,6 @@ files = [ name = "comm" version = "0.1.2" description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -740,7 +707,6 @@ test = ["pytest"] name = "contourpy" version = "1.0.7" description = "Python library for calculating contours of 2D quadrilateral grids" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -815,7 +781,6 @@ test-no-images = ["pytest"] name = "cycler" version = "0.11.0" description = "Composable style cycles" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -827,7 +792,6 @@ files = [ name = "dataclasses" version = "0.6" description = "A backport of the dataclasses module for Python 3.6" -category = "main" optional = false python-versions = "*" files = [ @@ -839,7 +803,6 @@ files = [ name = "debugpy" version = "1.6.5" description = "An implementation of the Debug Adapter Protocol for Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -867,7 +830,6 @@ files = [ name = "decorator" version = "5.1.1" description = "Decorators for Humans" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -879,7 +841,6 @@ files = [ name = "defusedxml" version = "0.7.1" description = "XML bomb protection for Python stdlib modules" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -891,7 +852,6 @@ files = [ name = "dicom2nifti" version = "2.4.7" description = "package for converting dicom files to nifti" -category = "main" optional = true python-versions = "*" files = [ @@ -910,7 +870,6 @@ scipy = "*" name = "dill" version = "0.3.6" description = "serialize all of python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -925,7 +884,6 @@ graph = ["objgraph (>=1.7.2)"] name = "docutils" version = "0.19" description = "Docutils -- Python Documentation Utilities" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -937,7 +895,6 @@ files = [ name = "entrypoints" version = "0.4" description = "Discover and load entry points from installed packages." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -949,7 +906,6 @@ files = [ name = "executing" version = "1.2.0" description = "Get the currently executing AST node of a frame, and other information" -category = "main" optional = false python-versions = "*" files = [ @@ -964,7 +920,6 @@ tests = ["asttokens", "littleutils", "pytest", "rich"] name = "fastjsonschema" version = "2.16.2" description = "Fastest Python implementation of JSON schema" -category = "dev" optional = false python-versions = "*" files = [ @@ -979,7 +934,6 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc name = "flask" version = "2.3.2" description = "A simple framework for building complex web applications." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1003,7 +957,6 @@ dotenv = ["python-dotenv"] name = "flask-restful" version = "0.3.9" description = "Simple framework for creating REST APIs" -category = "main" optional = true python-versions = "*" files = [ @@ -1024,7 +977,6 @@ docs = ["sphinx"] name = "flask-sqlalchemy" version = "2.5.1" description = "Adds SQLAlchemy support to your Flask application." -category = "main" optional = false python-versions = ">= 2.7, != 3.0.*, != 3.1.*, != 3.2.*, != 3.3.*" files = [ @@ -1040,7 +992,6 @@ SQLAlchemy = ">=0.8.0" name = "fonttools" version = "4.38.0" description = "Tools to manipulate font files" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1066,7 +1017,6 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] name = "fqdn" version = "1.5.1" description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" -category = "dev" optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" files = [ @@ -1078,7 +1028,6 @@ files = [ name = "furo" version = "2022.12.7" description = "A clean customisable Sphinx documentation theme." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1096,7 +1045,6 @@ sphinx-basic-ng = "*" name = "future" version = "0.18.3" description = "Clean single-source support for Python 3 and 2" -category = "main" optional = true python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1107,7 +1055,6 @@ files = [ name = "greenlet" version = "2.0.1" description = "Lightweight in-process concurrent programming" -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" files = [ @@ -1181,7 +1128,6 @@ test = ["faulthandler", "objgraph", "psutil"] name = "gunicorn" version = "20.1.0" description = "WSGI HTTP Server for UNIX" -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -1202,7 +1148,6 @@ tornado = ["tornado (>=0.2)"] name = "idna" version = "3.4" description = "Internationalized Domain Names in Applications (IDNA)" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -1214,7 +1159,6 @@ files = [ name = "imageio" version = "2.24.0" description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1247,7 +1191,6 @@ tifffile = ["tifffile"] name = "imagesize" version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1259,7 +1202,6 @@ files = [ name = "importlib-metadata" version = "6.0.0" description = "Read metadata from Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1279,7 +1221,6 @@ testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packag name = "importlib-resources" version = "5.10.2" description = "Read resources from Python packages" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1298,7 +1239,6 @@ testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-chec name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1310,7 +1250,6 @@ files = [ name = "ipykernel" version = "6.20.2" description = "IPython Kernel for Jupyter" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1343,7 +1282,6 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio" name = "ipython" version = "8.10.0" description = "IPython: Productive Interactive Computing" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1382,7 +1320,6 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pa name = "ipython-genutils" version = "0.2.0" description = "Vestigial utilities from IPython" -category = "dev" optional = false python-versions = "*" files = [ @@ -1394,7 +1331,6 @@ files = [ name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1409,7 +1345,6 @@ arrow = ">=0.15.0" name = "isort" version = "5.11.4" description = "A Python utility / library to sort Python imports." -category = "dev" optional = false python-versions = ">=3.7.0" files = [ @@ -1427,7 +1362,6 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] name = "itsdangerous" version = "2.1.2" description = "Safely pass data to untrusted environments and back." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1439,7 +1373,6 @@ files = [ name = "jedi" version = "0.18.2" description = "An autocompletion tool for Python that can be used for text editors." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1459,7 +1392,6 @@ testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] name = "jinja2" version = "3.1.2" description = "A very fast and expressive template engine." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1477,7 +1409,6 @@ i18n = ["Babel (>=2.7)"] name = "joblib" version = "1.2.0" description = "Lightweight pipelining with Python functions" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1489,7 +1420,6 @@ files = [ name = "json5" version = "0.9.11" description = "A Python implementation of the JSON5 data format." -category = "dev" optional = false python-versions = "*" files = [ @@ -1504,7 +1434,6 @@ dev = ["hypothesis"] name = "jsonpointer" version = "2.3" description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1516,7 +1445,6 @@ files = [ name = "jsonschema" version = "4.17.3" description = "An implementation of JSON Schema validation for Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1546,7 +1474,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jupyter-client" version = "7.4.9" description = "Jupyter protocol implementation and client libraries" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1571,7 +1498,6 @@ test = ["codecov", "coverage", "ipykernel (>=6.12)", "ipython", "mypy", "pre-com name = "jupyter-core" version = "5.1.3" description = "Jupyter core package. A base package on which Jupyter projects rely." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1592,7 +1518,6 @@ test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] name = "jupyter-events" version = "0.6.3" description = "Jupyter Event System library" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1617,7 +1542,6 @@ test = ["click", "coverage", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>= name = "jupyter-server" version = "2.1.0" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1630,7 +1554,7 @@ anyio = ">=3.1.0,<4" argon2-cffi = "*" jinja2 = "*" jupyter-client = ">=7.4.4" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" jupyter-events = ">=0.4.0" jupyter-server-terminals = "*" nbconvert = ">=6.4.4" @@ -1653,7 +1577,6 @@ test = ["ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", " name = "jupyter-server-terminals" version = "0.4.4" description = "A Jupyter Server Extension Providing Terminals." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1673,7 +1596,6 @@ test = ["coverage", "jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-cov", name = "jupyterlab" version = "3.5.2" description = "JupyterLab computational environment" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1700,7 +1622,6 @@ test = ["check-manifest", "coverage", "jupyterlab-server[test]", "pre-commit", " name = "jupyterlab-pygments" version = "0.2.2" description = "Pygments theme using JupyterLab CSS variables" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1712,7 +1633,6 @@ files = [ name = "jupyterlab-server" version = "2.19.0" description = "A set of server components for JupyterLab and JupyterLab like applications." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1739,7 +1659,6 @@ test = ["codecov", "ipykernel", "jupyterlab-server[openapi]", "openapi-spec-vali name = "kiwisolver" version = "1.4.4" description = "A fast implementation of the Cassowary constraint solver" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1817,7 +1736,6 @@ files = [ name = "kombu" version = "5.2.4" description = "Messaging library for Python." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1849,7 +1767,6 @@ zookeeper = ["kazoo (>=1.3.1)"] name = "lazy-object-proxy" version = "1.9.0" description = "A fast and thorough lazy object proxy." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1895,7 +1812,6 @@ files = [ name = "linecache2" version = "1.0.0" description = "Backports of the linecache module" -category = "main" optional = true python-versions = "*" files = [ @@ -1907,7 +1823,6 @@ files = [ name = "lxml" version = "4.9.2" description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*" files = [ @@ -2000,7 +1915,6 @@ source = ["Cython (>=0.29.7)"] name = "m2r2" version = "0.3.3" description = "Markdown and reStructuredText in a single file." -category = "dev" optional = false python-versions = "*" files = [ @@ -2016,7 +1930,6 @@ mistune = "0.8.4" name = "markupsafe" version = "2.1.1" description = "Safely add untrusted strings to HTML/XML markup." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2066,7 +1979,6 @@ files = [ name = "matplotlib" version = "3.6.3" description = "Python plotting package" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2128,7 +2040,6 @@ python-dateutil = ">=2.7" name = "matplotlib-inline" version = "0.1.6" description = "Inline Matplotlib backend for Jupyter" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -2143,7 +2054,6 @@ traitlets = "*" name = "mccabe" version = "0.7.0" description = "McCabe checker, plugin for flake8" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2155,7 +2065,6 @@ files = [ name = "medpy" version = "0.4.0" description = "Medical image processing in Python" -category = "main" optional = true python-versions = "*" files = [ @@ -2171,7 +2080,6 @@ SimpleITK = ">=1.1.0" name = "mistune" version = "0.8.4" description = "The fastest markdown parser in pure Python" -category = "dev" optional = false python-versions = "*" files = [ @@ -2183,7 +2091,6 @@ files = [ name = "mypy-extensions" version = "0.4.3" description = "Experimental type system extensions for programs checked with the mypy typechecker." -category = "dev" optional = false python-versions = "*" files = [ @@ -2195,7 +2102,6 @@ files = [ name = "nbclassic" version = "0.4.8" description = "A web-based notebook environment for interactive computing" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2231,7 +2137,6 @@ test = ["coverage", "nbval", "pytest", "pytest-cov", "pytest-playwright", "pytes name = "nbclient" version = "0.7.2" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." -category = "dev" optional = false python-versions = ">=3.7.0" files = [ @@ -2241,7 +2146,7 @@ files = [ [package.dependencies] jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" nbformat = ">=5.1" traitlets = ">=5.3" @@ -2254,7 +2159,6 @@ test = ["ipykernel", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>= name = "nbconvert" version = "6.5.4" description = "Converting Jupyter Notebooks" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2292,7 +2196,6 @@ webpdf = ["pyppeteer (>=1,<1.1)"] name = "nbformat" version = "5.7.3" description = "The Jupyter Notebook format" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2314,7 +2217,6 @@ test = ["pep440", "pre-commit", "pytest", "testpath"] name = "nbsphinx" version = "0.8.11" description = "Jupyter Notebook Tools for Sphinx" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2334,7 +2236,6 @@ traitlets = ">=5" name = "nbstripout" version = "0.3.9" description = "Strips outputs from Jupyter and IPython notebooks" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2349,7 +2250,6 @@ nbformat = "*" name = "nest-asyncio" version = "1.5.6" description = "Patch asyncio to allow nested event loops" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2361,7 +2261,6 @@ files = [ name = "networkx" version = "3.0" description = "Python package for creating and manipulating graphs and networks" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2380,7 +2279,6 @@ test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"] name = "nibabel" version = "5.0.0" description = "Access a multitude of neuroimaging data formats" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -2411,7 +2309,6 @@ zstd = ["pyzstd (>=0.14.3)"] name = "nnunet" version = "1.7.0" description = "nnU-Net. Framework for out-of-the box biomedical image segmentation." -category = "main" optional = true python-versions = "*" files = [ @@ -2438,7 +2335,6 @@ tqdm = "*" name = "notebook" version = "6.5.2" description = "A web-based notebook environment for interactive computing" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2473,7 +2369,6 @@ test = ["coverage", "nbval", "pytest", "pytest-cov", "requests", "requests-unixs name = "notebook-shim" version = "0.2.2" description = "A shim layer for notebook traits and config" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2491,7 +2386,6 @@ test = ["pytest", "pytest-console-scripts", "pytest-tornasync"] name = "numpy" version = "1.24.1" description = "Fundamental package for array computing in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2529,7 +2423,6 @@ files = [ name = "nvidia-cublas-cu11" version = "11.10.3.66" description = "CUBLAS native runtime libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -2545,7 +2438,6 @@ wheel = "*" name = "nvidia-cuda-nvrtc-cu11" version = "11.7.99" description = "NVRTC native runtime libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -2562,7 +2454,6 @@ wheel = "*" name = "nvidia-cuda-runtime-cu11" version = "11.7.99" description = "CUDA Runtime native Libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -2578,7 +2469,6 @@ wheel = "*" name = "nvidia-cudnn-cu11" version = "8.5.0.96" description = "cuDNN runtime libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -2594,7 +2484,6 @@ wheel = "*" name = "opencv-python" version = "4.7.0.68" description = "Wrapper package for OpenCV python bindings." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2621,7 +2510,6 @@ numpy = [ name = "packaging" version = "23.0" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2633,7 +2521,6 @@ files = [ name = "pandas" version = "1.5.2" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2682,7 +2569,6 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] name = "pandocfilters" version = "1.5.0" description = "Utilities for writing pandoc filters in python" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -2694,7 +2580,6 @@ files = [ name = "parso" version = "0.8.3" description = "A Python Parser" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2710,7 +2595,6 @@ testing = ["docopt", "pytest (<6.0.0)"] name = "pathspec" version = "0.10.3" description = "Utility library for gitignore style pattern matching of file paths." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2722,7 +2606,6 @@ files = [ name = "pexpect" version = "4.8.0" description = "Pexpect allows easy control of interactive console applications." -category = "main" optional = false python-versions = "*" files = [ @@ -2737,7 +2620,6 @@ ptyprocess = ">=0.5" name = "pickleshare" version = "0.7.5" description = "Tiny 'shelve'-like database with concurrency support" -category = "main" optional = false python-versions = "*" files = [ @@ -2749,7 +2631,6 @@ files = [ name = "pillow" version = "9.4.0" description = "Python Imaging Library (Fork)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2840,7 +2721,6 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa name = "pkgutil-resolve-name" version = "1.3.10" description = "Resolve a name to an object." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2852,7 +2732,6 @@ files = [ name = "platformdirs" version = "2.6.2" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2868,7 +2747,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2)", "pytest- name = "pluggy" version = "1.0.0" description = "plugin and hook calling mechanisms for python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2884,7 +2762,6 @@ testing = ["pytest", "pytest-benchmark"] name = "pockets" version = "0.9.1" description = "A collection of helpful Python tools!" -category = "dev" optional = false python-versions = "*" files = [ @@ -2899,7 +2776,6 @@ six = ">=1.5.2" name = "prometheus-client" version = "0.15.0" description = "Python client for the Prometheus monitoring system." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2914,7 +2790,6 @@ twisted = ["twisted"] name = "prompt-toolkit" version = "3.0.36" description = "Library for building powerful interactive command lines in Python" -category = "main" optional = false python-versions = ">=3.6.2" files = [ @@ -2929,7 +2804,6 @@ wcwidth = "*" name = "psutil" version = "5.9.4" description = "Cross-platform lib for process and system monitoring in Python." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -2956,7 +2830,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "ptyprocess" version = "0.7.0" description = "Run a subprocess in a pseudo terminal" -category = "main" optional = false python-versions = "*" files = [ @@ -2968,7 +2841,6 @@ files = [ name = "pure-eval" version = "0.2.2" description = "Safely evaluate AST nodes without side effects" -category = "main" optional = false python-versions = "*" files = [ @@ -2983,7 +2855,6 @@ tests = ["pytest"] name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2995,7 +2866,6 @@ files = [ name = "pycparser" version = "2.21" description = "C parser in Python" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3007,7 +2877,6 @@ files = [ name = "pydicom" version = "2.3.1" description = "A pure Python package for reading and writing DICOM data" -category = "main" optional = false python-versions = ">=3.6.1" files = [ @@ -3022,7 +2891,6 @@ docs = ["matplotlib", "numpy", "numpydoc", "pillow", "sphinx", "sphinx-copybutto name = "pygments" version = "2.14.0" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3037,7 +2905,6 @@ plugins = ["importlib-metadata"] name = "pylint" version = "2.15.10" description = "python code static checker" -category = "dev" optional = false python-versions = ">=3.7.2" files = [ @@ -3067,7 +2934,6 @@ testutils = ["gitpython (>3)"] name = "pylint-flask-sqlalchemy" version = "0.2.0" description = "A Pylint plugin for improving code analysis when editing code using Flask-SQLAlchemy" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -3086,7 +2952,6 @@ dev = ["black", "bump2version", "gitchangelog", "mypy", "pystache"] name = "pymedphys" version = "0.38.0" description = "Medical Physics library" -category = "main" optional = true python-versions = ">=3.7,<4.0" files = [ @@ -3115,7 +2980,6 @@ user = ["Pillow (>=9.0.0)", "PyYAML", "attrs", "dbfread", "dicompyler-core", "fs name = "pynetdicom" version = "2.0.2" description = "A Python implementation of the DICOM networking protocol" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3135,7 +2999,6 @@ tests = ["pyfakefs", "pytest", "sqlalchemy"] name = "pyparsing" version = "3.0.9" description = "pyparsing module - Classes and methods to define and execute parsing grammars" -category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -3150,7 +3013,6 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pyrsistent" version = "0.19.3" description = "Persistent/Functional/Immutable data structures" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3187,7 +3049,6 @@ files = [ name = "pytest" version = "6.2.5" description = "pytest: simple powerful testing with Python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3212,7 +3073,6 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -3227,7 +3087,6 @@ six = ">=1.5" name = "python-gdcm" version = "3.0.20" description = "Grassroots DICOM runtime libraries" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -3278,7 +3137,6 @@ files = [ name = "python-json-logger" version = "2.0.4" description = "A python library adding a json log formatter" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -3290,7 +3148,6 @@ files = [ name = "pytz" version = "2022.7.1" description = "World timezone definitions, modern and historical" -category = "main" optional = false python-versions = "*" files = [ @@ -3302,7 +3159,6 @@ files = [ name = "pywavelets" version = "1.4.1" description = "PyWavelets, wavelet transform module" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3340,7 +3196,6 @@ numpy = ">=1.17.3" name = "pywin32" version = "305" description = "Python for Window Extensions" -category = "dev" optional = false python-versions = "*" files = [ @@ -3364,7 +3219,6 @@ files = [ name = "pywinpty" version = "2.0.10" description = "Pseudo terminal support for Windows from Python." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3380,7 +3234,6 @@ files = [ name = "pyyaml" version = "6.0" description = "YAML parser and emitter for Python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3430,7 +3283,6 @@ files = [ name = "pyzmq" version = "25.0.0" description = "Python bindings for 0MQ" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3520,7 +3372,6 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""} name = "redis" version = "4.5.4" description = "Python client for Redis database and key-value store" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -3539,7 +3390,6 @@ ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)" name = "requests" version = "2.28.2" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7, <4" files = [ @@ -3561,7 +3411,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "rfc3339-validator" version = "0.1.4" description = "A pure python RFC3339 validator" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3576,7 +3425,6 @@ six = "*" name = "rfc3986-validator" version = "0.1.1" description = "Pure python rfc3986 validator" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3588,7 +3436,6 @@ files = [ name = "rt-utils" version = "1.2.7" description = "A small library for handling masks and RT-Structs" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3606,7 +3453,6 @@ pydicom = "*" name = "scikit-image" version = "0.19.3" description = "Image processing in Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3658,7 +3504,6 @@ test = ["asv", "codecov", "flake8", "matplotlib (>=3.0.3)", "pooch (>=1.3.0)", " name = "scikit-learn" version = "1.2.0" description = "A set of python modules for machine learning and data mining" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -3701,7 +3546,6 @@ tests = ["black (>=22.3.0)", "flake8 (>=3.8.2)", "matplotlib (>=3.1.3)", "mypy ( name = "scipy" version = "1.9.3" description = "Fundamental algorithms for scientific computing in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3740,7 +3584,6 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki name = "send2trash" version = "1.8.0" description = "Send file to trash natively under Mac OS X, Windows and Linux." -category = "dev" optional = false python-versions = "*" files = [ @@ -3757,7 +3600,6 @@ win32 = ["pywin32"] name = "setuptools" version = "66.0.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3774,7 +3616,6 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs ( name = "simpleitk" version = "2.2.1" description = "SimpleITK is a simplified interface to the Insight Toolkit (ITK) for image registration and segmentation" -category = "main" optional = false python-versions = "*" files = [ @@ -3808,7 +3649,6 @@ files = [ name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3820,7 +3660,6 @@ files = [ name = "sklearn" version = "0.0.post1" description = "deprecated sklearn package, use scikit-learn instead" -category = "main" optional = true python-versions = "*" files = [ @@ -3831,7 +3670,6 @@ files = [ name = "sniffio" version = "1.3.0" description = "Sniff out which async library your code is running under" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3843,7 +3681,6 @@ files = [ name = "snowballstemmer" version = "2.2.0" description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." -category = "dev" optional = false python-versions = "*" files = [ @@ -3855,7 +3692,6 @@ files = [ name = "soupsieve" version = "2.3.2.post1" description = "A modern CSS selector implementation for Beautiful Soup." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3867,7 +3703,6 @@ files = [ name = "sphinx" version = "5.3.0" description = "Python documentation generator" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3903,7 +3738,6 @@ test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"] name = "sphinx-basic-ng" version = "1.0.0b1" description = "A modern skeleton for Sphinx themes." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3921,7 +3755,6 @@ docs = ["furo", "ipython", "myst-parser", "sphinx-copybutton", "sphinx-inline-ta name = "sphinx-click" version = "4.4.0" description = "Sphinx extension that automatically documents click applications" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3938,7 +3771,6 @@ sphinx = ">=2.0" name = "sphinx-theme" version = "1.0" description = "Sphinx documentation theme based on readthedocs.org" -category = "dev" optional = false python-versions = "*" files = [ @@ -3950,7 +3782,6 @@ files = [ name = "sphinxcontrib-applehelp" version = "1.0.3" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3966,7 +3797,6 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.2" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -3982,7 +3812,6 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.0" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3998,7 +3827,6 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -4013,7 +3841,6 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-napoleon" version = "0.7" description = "Sphinx \"napoleon\" extension." -category = "dev" optional = false python-versions = "*" files = [ @@ -4029,7 +3856,6 @@ six = ">=1.5.2" name = "sphinxcontrib-qthelp" version = "1.0.3" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -4045,7 +3871,6 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -4061,7 +3886,6 @@ test = ["pytest"] name = "sqlalchemy" version = "1.4.46" description = "Database Abstraction Library" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -4109,7 +3933,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\")"} [package.extras] aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] @@ -4136,7 +3960,6 @@ sqlcipher = ["sqlcipher3-binary"] name = "stack-data" version = "0.6.2" description = "Extract data from python stack frames and tracebacks for informative displays" -category = "main" optional = false python-versions = "*" files = [ @@ -4156,7 +3979,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] name = "terminado" version = "0.17.1" description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4177,7 +3999,6 @@ test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"] name = "threadpoolctl" version = "3.1.0" description = "threadpoolctl" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -4189,7 +4010,6 @@ files = [ name = "tifffile" version = "2022.10.10" description = "Read and write TIFF files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4207,7 +4027,6 @@ all = ["fsspec", "imagecodecs (>=2022.2.22)", "lxml", "matplotlib (>=3.3)", "zar name = "tinycss2" version = "1.2.1" description = "A tiny CSS parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4226,7 +4045,6 @@ test = ["flake8", "isort", "pytest"] name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" -category = "dev" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -4238,7 +4056,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4250,7 +4067,6 @@ files = [ name = "tomlkit" version = "0.11.6" description = "Style preserving TOML library" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4262,7 +4078,6 @@ files = [ name = "torch" version = "1.13.1" description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration" -category = "main" optional = true python-versions = ">=3.7.0" files = [ @@ -4303,7 +4118,6 @@ opt-einsum = ["opt-einsum (>=3.3)"] name = "tornado" version = "6.3.2" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." -category = "dev" optional = false python-versions = ">= 3.8" files = [ @@ -4324,7 +4138,6 @@ files = [ name = "tqdm" version = "4.64.1" description = "Fast, Extensible Progress Meter" -category = "main" optional = true python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" files = [ @@ -4345,7 +4158,6 @@ telegram = ["requests"] name = "traceback2" version = "1.4.0" description = "Backports of the traceback module" -category = "main" optional = true python-versions = "*" files = [ @@ -4360,7 +4172,6 @@ linecache2 = "*" name = "traitlets" version = "5.8.1" description = "Traitlets Python configuration system" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4376,7 +4187,6 @@ test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] name = "typing-extensions" version = "4.4.0" description = "Backported and Experimental Type Hints for Python 3.7+" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4388,7 +4198,6 @@ files = [ name = "unittest2" version = "1.1.0" description = "The new features in unittest backported to Python 2.4+." -category = "main" optional = true python-versions = "*" files = [ @@ -4405,7 +4214,6 @@ traceback2 = "*" name = "uri-template" version = "1.2.0" description = "RFC 6570 URI Template Processor" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4420,7 +4228,6 @@ dev = ["flake8 (<4.0.0)", "flake8-annotations", "flake8-bugbear", "flake8-commas name = "urllib3" version = "1.26.14" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -4437,7 +4244,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "vine" version = "5.0.0" description = "Promises, promises, promises." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -4449,7 +4255,6 @@ files = [ name = "vtk" version = "9.2.5" description = "VTK is an open-source toolkit for 3D computer graphics, image processing, and visualization" -category = "main" optional = true python-versions = "*" files = [ @@ -4487,7 +4292,6 @@ web = ["wslink (>=1.0.4)"] name = "watchdog" version = "2.2.1" description = "Filesystem events monitoring" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4528,7 +4332,6 @@ watchmedo = ["PyYAML (>=3.10)"] name = "wcwidth" version = "0.2.6" description = "Measures the displayed width of unicode strings in a terminal" -category = "main" optional = false python-versions = "*" files = [ @@ -4540,7 +4343,6 @@ files = [ name = "webcolors" version = "1.12" description = "A library for working with color names and color values formats defined by HTML and CSS." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4552,7 +4354,6 @@ files = [ name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "dev" optional = false python-versions = "*" files = [ @@ -4564,7 +4365,6 @@ files = [ name = "websocket-client" version = "1.4.2" description = "WebSocket client for Python with low level API options" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4581,7 +4381,6 @@ test = ["websockets"] name = "werkzeug" version = "2.3.3" description = "The comprehensive WSGI web application library." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4599,7 +4398,6 @@ watchdog = ["watchdog (>=2.3)"] name = "wheel" version = "0.38.4" description = "A built-package format for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -4614,7 +4412,6 @@ test = ["pytest (>=3.0.0)"] name = "wrapt" version = "1.14.1" description = "Module for decorators, wrappers and monkey patching." -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -4688,7 +4485,6 @@ files = [ name = "zipp" version = "3.11.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4701,8 +4497,8 @@ docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [extras] -backend = ["Flask", "Flask-RESTful", "Flask-SQLAlchemy", "celery", "redis", "psutil", "gunicorn", "Jinja2", "pymedphys"] -cardiac = ["vtk", "nnunet"] +backend = ["Flask", "Flask-RESTful", "Flask-SQLAlchemy", "Jinja2", "celery", "gunicorn", "psutil", "pymedphys", "redis"] +cardiac = ["nnunet", "vtk"] nnunet = ["nnunet"] [metadata] From 43ef6d2723d4ec633d1686e216498c41c9ce8933 Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Mon, 14 Aug 2023 09:20:53 +1000 Subject: [PATCH 09/32] Update deprecated matplotlib colormaps --- platipy/dicom/io/nifti_to_rtstruct.py | 10 ++-- platipy/imaging/utils/io.py | 6 +- platipy/imaging/visualisation/animation.py | 18 ++---- platipy/imaging/visualisation/comparison.py | 13 +++-- platipy/imaging/visualisation/dose.py | 15 ++--- platipy/imaging/visualisation/utils.py | 7 +-- platipy/imaging/visualisation/visualiser.py | 62 ++++++--------------- 7 files changed, 48 insertions(+), 83 deletions(-) diff --git a/platipy/dicom/io/nifti_to_rtstruct.py b/platipy/dicom/io/nifti_to_rtstruct.py index c87375fc..027a4641 100644 --- a/platipy/dicom/io/nifti_to_rtstruct.py +++ b/platipy/dicom/io/nifti_to_rtstruct.py @@ -19,6 +19,7 @@ import SimpleITK as sitk import numpy as np import logging +import matplotlib from matplotlib import cm from rt_utils import RTStructBuilder @@ -26,7 +27,9 @@ logger = logging.getLogger(__name__) -def convert_nifti(dcm_path, mask_input, output_file, color_map=cm.get_cmap("rainbow")): +def convert_nifti( + dcm_path, mask_input, output_file, color_map=matplotlib.colormaps.get_cmap("rainbow") +): """Convert a set of masks to a DICOM RTStruct object. This function now utilises the rt-utils package: https://github.com/qurit/rt-utils @@ -37,8 +40,8 @@ def convert_nifti(dcm_path, mask_input, output_file, color_map=cm.get_cmap("rain mask_input (dict|list): A dictionary containing the name as key and image as value. Or a list of string with comma separated name and mask paths (name,path) output_file (str|pathlib.Path): The path to the file to write the RTStruct - color_map (matplotlib.colors.Colormap, optional): Colormap to use for output. Defaults to - cm.get_cmap("rainbow"). + color_map (matplotlib.colors.Colormap, optional): Colormap to use for output. Defaults to + matplotlib.colormaps.get_cmap("rainbow"). """ logger.info("Will convert the following Nifti masks to RTStruct:") @@ -65,7 +68,6 @@ def convert_nifti(dcm_path, mask_input, output_file, color_map=cm.get_cmap("rain rtstruct = RTStructBuilder.create_new(dicom_series_path=str(dcm_series_path)) for mask_name in masks: - # Use a hash of the name to get the color from the supplied color map color = color_map(hash(mask_name) % 256) color = color[:3] diff --git a/platipy/imaging/utils/io.py b/platipy/imaging/utils/io.py index ee315d98..26c68656 100644 --- a/platipy/imaging/utils/io.py +++ b/platipy/imaging/utils/io.py @@ -2,13 +2,14 @@ import numpy as np import SimpleITK as sitk +import matplotlib import matplotlib.colors as mcolors def write_nrrd_structure_set( masks, output_file="structure_set.nrrd", - colormap=cm.get_cmap("rainbow"), + colormap=matplotlib.colormaps.get_cmap("rainbow"), use_compression=True, compression_level=9, ): @@ -20,7 +21,7 @@ def write_nrrd_structure_set( "structure_set.nrrd". colormap (matplotlib.colors.Colormap | dict, optional): Colormap to use for output. Can also use a dictionary with keys as structure names and values as colors. - Defaults to cm.get_cmap("rainbow"). + Defaults to matplotlib.colormaps.get_cmap("rainbow"). use_compression (bool, optional): Used by SimpleITK's WriteImage function to enable compression when writing output file. Defaults to True. compression_level (int, optional): Used by SimpleITK's WriteImage function to specify how @@ -52,7 +53,6 @@ def write_nrrd_structure_set( structure_value = 1 dim = 0 if len(all_arr) > 0: - # Check if this structure has space in the current dim # Append a new dim if not struct_added = False diff --git a/platipy/imaging/visualisation/animation.py b/platipy/imaging/visualisation/animation.py index 87b91a2c..f41efe84 100644 --- a/platipy/imaging/visualisation/animation.py +++ b/platipy/imaging/visualisation/animation.py @@ -47,7 +47,6 @@ def setup(self, fig, dpi, frame_prefix): self.temp_prefix, self.frame_format = self.outfile.split(".") def grab_frame(self, **savefig_kwargs): - with self._frame_sink() as myframesink: self.fig.savefig(myframesink, format="png", dpi=self.dpi, **savefig_kwargs) @@ -62,9 +61,9 @@ def generate_animation_from_image_sequence( contour_list=None, scalar_list=None, figure_size_in=6, - image_cmap=plt.cm.get_cmap("Greys_r"), - contour_cmap=plt.cm.get_cmap("jet"), - scalar_cmap=plt.cm.get_cmap("magma"), + image_cmap=matplotlib.colormaps.get_cmap("Greys_r"), + contour_cmap=matplotlib.colormaps.get_cmap("jet"), + scalar_cmap=matplotlib.colormaps.get_cmap("magma"), image_window=[-1000, 800], scalar_min=None, scalar_max=None, @@ -84,11 +83,11 @@ def generate_animation_from_image_sequence( (overlay as contours). Defaults to False. figure_size_in (int, optional): Size of the figure. Defaults to 6. image_cmap (matplotlib.colors.ListedColormap, optional): Colormap to use for the image. - Defaults to plt.cm.get_cmap("Greys_r"). + Defaults to matplotlib.colormaps.get_cmap("Greys_r"). contour_cmap (matplotlib.colors.ListedColormap, optional): Colormap to use for contours. - Defaults to plt.cm.get_cmap("jet"). + Defaults to matplotlib.colormaps.get_cmap("jet"). scalar_cmap (matplotlib.colors.ListedColormap, optional): Colormap to use for scalar field. - Defaults to plt.cm.get_cmap("magma"). + Defaults to matplotlib.colormaps.get_cmap("magma"). image_window (list, optional): Image intensity window (mininmum, range). Defaults to [-1000, 800]. scalar_min (bool, optional): Minimum scalar value to show. Defaults to False. @@ -131,7 +130,6 @@ def generate_animation_from_image_sequence( # We now deal with the contours # These can be given as a list of sitk.Image objects or a list of dicts {"name":sitk.Image} if contour_list: - if isinstance(contour_list[0], sitk.Image): plot_dict = {"_": contour_list[0]} contour_labels = False @@ -146,7 +144,6 @@ def generate_animation_from_image_sequence( color_list = [color_map[i] for i in range(len(plot_dict.values()))] for ctr_key, color in zip(plot_dict.keys(), color_list): - display_contours = ax.contour( sitk.GetArrayFromImage(plot_dict[ctr_key]), colors=[color], @@ -165,7 +162,6 @@ def generate_animation_from_image_sequence( ) if scalar_list: - if not scalar_min: scalar_min = np.min([sitk.GetArrayFromImage(i) for i in scalar_list]) if not scalar_max: @@ -188,7 +184,6 @@ def generate_animation_from_image_sequence( # The animate function does (you guessed it) the animation def animate(i): - # Update the imaging data nda = sitk.GetArrayFromImage(image_list[i]) display_image.set_data(nda) @@ -212,7 +207,6 @@ def animate(i): color_list = [color_map[i] for i in range(len(plot_dict.values()))] for contour, color in zip(plot_dict.values(), color_list): - ax.contour( sitk.GetArrayFromImage(contour), colors=[color], diff --git a/platipy/imaging/visualisation/comparison.py b/platipy/imaging/visualisation/comparison.py index 46cc1615..d79d469b 100644 --- a/platipy/imaging/visualisation/comparison.py +++ b/platipy/imaging/visualisation/comparison.py @@ -19,6 +19,7 @@ import pandas as pd +import matplotlib import matplotlib.lines as mlines import matplotlib as plt import matplotlib.colors as mcolors @@ -47,7 +48,7 @@ def contour_comparison( title="", subtitle="", subsubtitle="", - contour_cmap=plt.cm.get_cmap("rainbow"), + contour_cmap=matplotlib.colormaps.get_cmap("rainbow"), structure_name_dict=None, img_vis_kw=None, ): @@ -75,7 +76,7 @@ def contour_comparison( subsubtitle (str, optional): Subsubtitle of the plot, set to "" to remove. Defaults to "SUBSUBTITLE TEXT". contour_cmap (plt.cm.colormap, optional): Contour colormap. - Defaults to plt.cm.get_cmap("rainbow"). + Defaults to matplotlib.colormaps.get_cmap("rainbow"). structure_name_dict (dict, optional): A "translation" dictionary used to overwrite the names of contours in the metric table. Defaults to using the names in the contour_dict. img_vis_kw (dict, optional): Passed to the ImageVisualiser class. Defaults to {}. @@ -92,7 +93,6 @@ def contour_comparison( img_vis_kw = {} if "cut" not in img_vis_kw: - cut = None # first check if the user has specified a structure @@ -132,14 +132,16 @@ def contour_comparison( colors_a = { s + "a": c for s, c in zip( - s_select, plt.cm.get_cmap(contour_cmap)(np.linspace(0, 1, len(s_select))) + s_select, + matplotlib.colormaps.get_cmap(contour_cmap)(np.linspace(0, 1, len(s_select))), ) } colors_b = { s + "b": c for s, c in zip( - s_select, plt.cm.get_cmap(contour_cmap)(np.linspace(0, 1, len(s_select))) + s_select, + matplotlib.colormaps.get_cmap(contour_cmap)(np.linspace(0, 1, len(s_select))), ) } @@ -264,7 +266,6 @@ def contour_comparison( # Geometry fixes for row in range(len(rows) + 1): - table[row, 0].set_width(0.1) table[row, 1].set_width(0.1) table[row, 2].set_width(0.1) diff --git a/platipy/imaging/visualisation/dose.py b/platipy/imaging/visualisation/dose.py index e88241c6..4a3c6897 100644 --- a/platipy/imaging/visualisation/dose.py +++ b/platipy/imaging/visualisation/dose.py @@ -2,6 +2,7 @@ import numpy as np import SimpleITK as sitk +import matplotlib import matplotlib.pyplot as plt from platipy.imaging.label.utils import get_com @@ -58,8 +59,8 @@ def visualise_dose( structure_for_limits=None, expansion_for_limits=10, title="", - contour_cmap=plt.cm.get_cmap("rainbow"), - dose_cmap=plt.cm.get_cmap("inferno"), + contour_cmap=matplotlib.colormaps.get_cmap("rainbow"), + dose_cmap=matplotlib.colormaps.get_cmap("inferno"), structure_name_dict=None, img_vis_kw=None, ): @@ -87,9 +88,9 @@ def visualise_dose( to 10. title (str, optional): Title to display on visualisation. Defaults to "". contour_cmap (plt.cm.colormap, optional): Matplotlib color map to use for contour colors. - Defaults to plt.cm.get_cmap("rainbow"). + Defaults to matplotlib.colormaps.get_cmap("rainbow"). dose_cmap (plt.cm.colormap, optional): Matplotlib color map to use for dose colors. - Defaults to plt.cm.get_cmap("inferno"). + Defaults to matplotlib.colormaps.get_cmap("inferno"). structure_name_dict (dict, optional): Dictionary to map alternative structure names. Defaults to None. img_vis_kw (dict, optional): Dictionary of keyword arguments to pass to ImageVisualiser. @@ -111,17 +112,14 @@ def visualise_dose( df_metrics = dvh[["label", "mean"]] if d_points is not None: - df_metrics_d = calculate_d_x(dvh, d_points) df_metrics = df_metrics.merge(df_metrics_d) if v_points is not None: - df_metrics_v = calculate_v_x(dvh, v_points) df_metrics = df_metrics.merge(df_metrics_v) if d_cc_points is not None: - df_metrics_d_cc = calculate_d_cc_x(dvh, d_cc_points) df_metrics = df_metrics.merge(df_metrics_d_cc) @@ -198,7 +196,7 @@ def visualise_dose( for _, row in df_metrics.iterrows(): cell_text.append([f"{s:.2f}" for s in row.values]) - colors = list(plt.cm.get_cmap(contour_cmap)(np.linspace(0, 1, len(rows)))) + colors = list(matplotlib.colormaps.get_cmap(contour_cmap)(np.linspace(0, 1, len(rows)))) # Create the table table = ax.table( @@ -221,7 +219,6 @@ def visualise_dose( # Geometry fixes for row in range(len(rows) + 1): - for c in range(len(columns)): table[row, c].set_width(0.1) if row > 0: diff --git a/platipy/imaging/visualisation/utils.py b/platipy/imaging/visualisation/utils.py index 99fcd34f..f2abfde5 100644 --- a/platipy/imaging/visualisation/utils.py +++ b/platipy/imaging/visualisation/utils.py @@ -17,6 +17,7 @@ import numpy as np import SimpleITK as sitk +import matplotlib import matplotlib.pyplot as plt from platipy.imaging.utils.crop import label_to_roi @@ -52,7 +53,7 @@ def __init__( self, image, name, - colormap=plt.cm.get_cmap("Spectral"), + colormap=matplotlib.colormaps.get_cmap("Spectral"), alpha=0.75, min_value=False, max_value=False, @@ -83,7 +84,7 @@ def __init__( image, min_value=False, max_value=False, - colormap=plt.cm.get_cmap("Spectral"), + colormap=matplotlib.colormaps.get_cmap("Spectral"), discrete_levels=False, mid_ticks=False, alpha=0.75, @@ -124,7 +125,6 @@ class VisualiseBoundingBox: """Class to represent the visualiation of a bounding box""" def __init__(self, bounding_box, name, color="r", linewidth=2): - if isinstance(bounding_box, sitk.Image): bounding_box = label_to_roi(bounding_box, return_as_list=True) @@ -258,7 +258,6 @@ def reorientate_vector_field(axis, vector_ax, vector_cor, vector_sag, invert_fie def generate_comparison_colormix( image_list, arr_slice=None, window=(-250, 500), color_rotation=0.35 ): - #! TO DO - make this function take in more than two images # Will need to use polar coordinates for HSV colorspace addition diff --git a/platipy/imaging/visualisation/visualiser.py b/platipy/imaging/visualisation/visualiser.py index 0097ecfa..86e154bd 100644 --- a/platipy/imaging/visualisation/visualiser.py +++ b/platipy/imaging/visualisation/visualiser.py @@ -15,6 +15,7 @@ import warnings import logging +import matplotlib import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec @@ -58,7 +59,7 @@ def __init__( window=None, figure_size_in=10, limits=None, - colormap=plt.cm.get_cmap("Greys_r"), + colormap=matplotlib.colormaps.get_cmap("Greys_r"), origin="normal", projection=False, ): @@ -89,7 +90,6 @@ def __set_image(self, image): self.__image = image def __set_labelmap(self, labelmap, labels=None): - # TODO: Convert label map to binary masks for display raise NotImplementedError @@ -142,7 +142,7 @@ def add_contour( contour, name=None, color=None, - colormap=plt.cm.get_cmap("rainbow"), + colormap=matplotlib.colormaps.get_cmap("rainbow"), linewidth=2, linestyle="solid", show_legend=True, @@ -164,12 +164,10 @@ def add_contour( self.__show_legend = show_legend if isinstance(contour, dict): - if not all(map(lambda i: isinstance(i, sitk.Image), contour.values())): raise ValueError("When passing dict, all values must be of type SimpleITK.Image") for contour_name in contour: - if isinstance(color, dict): try: contour_color = color[contour_name] @@ -188,7 +186,6 @@ def add_contour( self.__contours.append(visualise_contour) elif isinstance(contour, sitk.Image): - # Use a default name if not specified if name is None: name = "contour" @@ -199,7 +196,6 @@ def add_contour( ) self.__contours.append(visualise_contour) else: - raise ValueError( "Contours should be represented as a dict with contour name as key " "and sitk.Image as value, or as an sitk.Image and passing the contour_name" @@ -211,7 +207,7 @@ def add_scalar_overlay( self, scalar_image, name=None, - colormap=plt.cm.get_cmap("cubehelix"), + colormap=matplotlib.colormaps.get_cmap("cubehelix"), alpha=0.75, min_value=False, max_value=False, @@ -228,8 +224,8 @@ def add_scalar_overlay( name (str, optional): Name to give the scalar image (only used if passing sitk.Image as scalar image). Defaults to None. colormap (matplotlib.colors.Colormap, optional): The colormap to be used when - overlaying this scalar image. Defaults - to plt.cm.get_cmap("cubehelix"). + overlaying this scalar image. Defaults to + matplotlib.colormaps.get_cmap("cubehelix"). alpha (float, optional): Alpha to apply to overlay. Defaults to 0.75. min_value (float, optional): Values below this value aren't rendered. Defaults to 0.1. @@ -241,7 +237,6 @@ def add_scalar_overlay( self.__show_colorbar = True if isinstance(scalar_image, dict): - if not all(map(lambda i: isinstance(i, sitk.Image), scalar_image.values())): raise ValueError("When passing dict, all values must be of type SimpleITK.Image") @@ -262,7 +257,6 @@ def add_scalar_overlay( self.__scalar_overlays.append(visualise_scalar) elif isinstance(scalar_image, sitk.Image): - # Use a default name if not specified if not name: name = "Value" @@ -283,7 +277,6 @@ def add_scalar_overlay( ) self.__scalar_overlays.append(visualise_scalar) else: - raise ValueError( "Contours should be represented as a dict with contour name as key " "and sitk.Image as value, or as an sitk.Image and passing the contour_name" @@ -294,7 +287,7 @@ def add_vector_overlay( vector_image, min_value=False, max_value=False, - colormap=plt.cm.get_cmap("inferno"), + colormap=matplotlib.colormaps.get_cmap("inferno"), discrete_levels=False, mid_ticks=False, alpha=0.75, @@ -312,8 +305,7 @@ def add_vector_overlay( name (str, optional): Name to give the vector field (only used if passing sitk.Image as vector field). Defaults to None. colormap (matplotlib.colors.Colormap, optional): The colormap to be used when - overlaying this vector field. Defaults - to plt.cm.get_cmap("inferno"). + overlaying this vector field. Defaults to matplotlib.colormaps.get_cmap("inferno"). alpha (float, optional): Alpha to apply to overlay vectors. Defaults to 0.75. arrow_scale (float, optional): Relative scaling of vectors. Defaults to 1. arrow_width (float, optional): Width of vector field arrow. Defaults to 1. @@ -332,7 +324,6 @@ def add_vector_overlay( isinstance(vector_image, sitk.Image) and vector_image.GetNumberOfComponentsPerPixel() > 1 ): - # Use a default name if not specified if not name: name = "Vector Field [mm]" @@ -355,7 +346,6 @@ def add_vector_overlay( ) self.__vector_overlays.append(visualise_vector_field) else: - raise ValueError("Vector field should be sitk.Image (of vector type).") def add_comparison_overlay(self, image, name=None, color_rotation=0.35): @@ -371,13 +361,11 @@ def add_comparison_overlay(self, image, name=None, color_rotation=0.35): """ if isinstance(image, sitk.Image): - visualise_comparison = VisualiseComparisonOverlay( image, name, color_rotation=color_rotation ) self.__comparison_overlays.append(visualise_comparison) else: - raise ValueError("Image should be sitk.Image.") def add_bounding_box(self, bounding_box, name=None, color="r", linewidth=2): @@ -401,7 +389,6 @@ def add_bounding_box(self, bounding_box, name=None, color="r", linewidth=2): self.__show_legend = True if isinstance(bounding_box, dict): - if not all( map( lambda i: isinstance(i, (list, tuple, sitk.Image)) and len(i) == 6, @@ -417,7 +404,6 @@ def add_bounding_box(self, bounding_box, name=None, color="r", linewidth=2): self.__bounding_boxes.append(visualise_bounding_box) elif isinstance(bounding_box, (list, tuple, sitk.Image)): - # Use a default name if not specified if name is None: name = "Bounding box" @@ -612,7 +598,6 @@ def _display_slice(self): } else: - if hasattr(self.__cut, "__iter__"): warnings.warn( "You have selected a single axis and multiple slice locations, attempting to " @@ -814,7 +799,6 @@ def _overlay_comparison(self): ) else: - if hasattr(self.__cut, "__iter__"): warnings.warn( "You have selected a single axis and multiple slice locations, attempting to " @@ -950,7 +934,6 @@ def _adjust_view(self): ax_ax_bbox = gs[0].get_position(self.__figure) for cax_index, cax in enumerate(cax_list): - cbar_width = ax_ax_bbox.width * 0.05 cax.set_position( @@ -1090,9 +1073,7 @@ def _overlay_contours(self): s_sag = return_slice("x", self.__cut[2]) for _, c_name in enumerate(plot_dict.keys()): - if not self.__projection: - contour_ax = sitk.GetArrayFromImage(plot_dict[c_name]).__getitem__(s_ax) contour_cor = sitk.GetArrayFromImage(plot_dict[c_name]).__getitem__(s_cor) contour_sag = sitk.GetArrayFromImage(plot_dict[c_name]).__getitem__(s_sag) @@ -1175,7 +1156,6 @@ def _overlay_scalar_field(self): """Overlay the scalar image onto the existing figure""" for scalar_index, scalar in enumerate(self.__scalar_overlays): - scalar_image = scalar.image nda = sitk.GetArrayFromImage(scalar_image) @@ -1193,7 +1173,7 @@ def _overlay_scalar_field(self): if scalar.discrete_levels: colormap_name = scalar.colormap.name - colormap = plt.cm.get_cmap(colormap_name, scalar.discrete_levels) + colormap = matplotlib.colormaps.get_cmap(colormap_name, scalar.discrete_levels) else: colormap = scalar.colormap @@ -1224,7 +1204,6 @@ def _overlay_scalar_field(self): projection = self.__projection if self.__axis == "ortho": - ax_ax, _, ax_cor, ax_sag = self.__figure.axes[:4] ax = ax_ax @@ -1317,7 +1296,6 @@ def _overlay_scalar_field(self): } else: - ax = self.__figure.axes[0] if not projection: @@ -1358,7 +1336,6 @@ def _overlay_scalar_field(self): ) if scalar.show_colorbar: - # divider = make_axes_locatable(ax_view) # cax = divider.append_axes("right", size="5%", pad=0.05) @@ -1403,9 +1380,7 @@ def _overlay_scalar_field(self): cbar.solids.set_alpha(1) if scalar.discrete_levels: - if scalar.mid_ticks: - delta_tick = (s_max - s_min) / scalar.discrete_levels cbar.set_ticks( np.linspace( @@ -1432,7 +1407,6 @@ def _overlay_vector_field(self): raise Warning("Vector overlay is not implemented in projection mode.") for vector_index, vector in enumerate(self.__vector_overlays): - image = vector.image colormap = vector.colormap alpha = vector.alpha @@ -1450,7 +1424,7 @@ def _overlay_vector_field(self): if vector.discrete_levels: colormap_name = vector.colormap.name - colormap = plt.cm.get_cmap(colormap_name, vector.discrete_levels) + colormap = matplotlib.colormaps.get_cmap(colormap_name, vector.discrete_levels) # Test types of axes axes = self.__figure.axes @@ -1470,7 +1444,11 @@ def _overlay_vector_field(self): vector_cor = vector_nda_slice[:, :, 1].T vector_sag = vector_nda_slice[:, :, 0].T - (vector_plot_x, vector_plot_y, vector_plot_z,) = reorientate_vector_field( + ( + vector_plot_x, + vector_plot_y, + vector_plot_z, + ) = reorientate_vector_field( self.__axis, vector_ax, vector_cor, @@ -1528,7 +1506,6 @@ def _overlay_vector_field(self): for plot_axes, im_axis, im_cut in zip( (ax_ax, ax_cor, ax_sag), ("z", "y", "x"), self.__cut ): - if not hasattr(subsample, "__iter__"): subsample = (subsample,) * 3 @@ -1579,7 +1556,6 @@ def _overlay_vector_field(self): ) if vector.show_colorbar: - # divider = make_axes_locatable(ax_view) # cax = divider.append_axes("right", size="5%", pad=0.05) @@ -1624,9 +1600,7 @@ def _overlay_vector_field(self): cbar.solids.set_alpha(1) if vector.discrete_levels: - if vector.mid_ticks: - delta_tick = (max_value - min_value) / vector.discrete_levels cbar.set_ticks( np.linspace( @@ -1649,7 +1623,6 @@ def _overlay_vector_field(self): ) def draw_bounding_box_on_axes(self, ax, view, box, add_label=True): - sag_0, cor_0, ax_0, sag_d, cor_d, ax_d = box.bounding_box from_points = None @@ -1687,7 +1660,6 @@ def _overlay_bounding_boxes(self): """ for box in self.__bounding_boxes: - # Test types of axes axes = self.__figure.axes[:4] if len(axes) < 4: @@ -1704,7 +1676,6 @@ def _add_legend(self): """Add a legend to the visualisation""" if len(self.__figure.axes) >= 4: - ax_ax = self.__figure.axes[0] ax_ax_position = ax_ax.get_position() y_pos_legend = (ax_ax_position.ymax + ax_ax_position.ymin) / 2 @@ -1743,11 +1714,12 @@ def _add_legend(self): approx_font_scaling = self.__figure_size / ( len(self.__contours) + len(self.__bounding_boxes) ) + fontsize = min([10, 16 * approx_font_scaling]) plt.figlegend( loc="center left", bbox_to_anchor=(x_pos_legend, y_pos_legend), - fontsize=min([10, 16 * approx_font_scaling]), + fontsize=fontsize, ncol=1, #!TODO modify this for large numbers of contours ) From 5d371c70edc19f836e2539ddcf66cdb88db05dc6 Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Mon, 14 Aug 2023 09:38:00 +1000 Subject: [PATCH 10/32] Update to new way of resampling colormap --- platipy/imaging/visualisation/visualiser.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/platipy/imaging/visualisation/visualiser.py b/platipy/imaging/visualisation/visualiser.py index 86e154bd..0208baee 100644 --- a/platipy/imaging/visualisation/visualiser.py +++ b/platipy/imaging/visualisation/visualiser.py @@ -1173,7 +1173,8 @@ def _overlay_scalar_field(self): if scalar.discrete_levels: colormap_name = scalar.colormap.name - colormap = matplotlib.colormaps.get_cmap(colormap_name, scalar.discrete_levels) + colormap = matplotlib.colormaps.get_cmap(colormap_name) + colormap = colormap.resampled(scalar.discrete_levels) else: colormap = scalar.colormap From e183f18b81ff75a75971a2a8543ec392f6795c96 Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Mon, 14 Aug 2023 10:26:13 +1000 Subject: [PATCH 11/32] Update poetry lock --- poetry.lock | 3659 +++++++++++++++++++++++++++------------------------ 1 file changed, 1920 insertions(+), 1739 deletions(-) diff --git a/poetry.lock b/poetry.lock index ea4e9a71..ef0e135c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,35 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. + +[[package]] +name = "aiofiles" +version = "22.1.0" +description = "File support for asyncio." +optional = false +python-versions = ">=3.7,<4.0" +files = [ + {file = "aiofiles-22.1.0-py3-none-any.whl", hash = "sha256:1142fa8e80dbae46bb6339573ad4c8c0841358f79c6eb50a493dceca14621bad"}, + {file = "aiofiles-22.1.0.tar.gz", hash = "sha256:9107f1ca0b2a5553987a94a3c9959fe5b491fdf731389aa5b7b1bd0733e32de6"}, +] + +[[package]] +name = "aiosqlite" +version = "0.19.0" +description = "asyncio bridge to the standard sqlite3 module" +optional = false +python-versions = ">=3.7" +files = [ + {file = "aiosqlite-0.19.0-py3-none-any.whl", hash = "sha256:edba222e03453e094a3ce605db1b970c4b3376264e56f32e2a4959f948d66a96"}, + {file = "aiosqlite-0.19.0.tar.gz", hash = "sha256:95ee77b91c8d2808bd08a59fbebf66270e9090c3d92ffbf260dc0db0b979577d"}, +] + +[package.extras] +dev = ["aiounittest (==1.4.1)", "attribution (==1.6.2)", "black (==23.3.0)", "coverage[toml] (==7.2.3)", "flake8 (==5.0.4)", "flake8-bugbear (==23.3.12)", "flit (==3.7.1)", "mypy (==1.2.0)", "ufmt (==2.1.0)", "usort (==1.0.6)"] +docs = ["sphinx (==6.1.3)", "sphinx-mdinclude (==0.5.3)"] [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -16,7 +41,6 @@ files = [ name = "amqp" version = "5.1.1" description = "Low-level AMQP client for Python (fork of amqplib)." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -31,7 +55,6 @@ vine = ">=5.0.0" name = "aniso8601" version = "9.0.1" description = "A library for parsing ISO 8601 strings." -category = "main" optional = true python-versions = "*" files = [ @@ -44,30 +67,29 @@ dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] [[package]] name = "anyio" -version = "3.6.2" +version = "3.7.1" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "dev" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7" files = [ - 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@@ nnunet = ["nnunet"] [metadata] lock-version = "2.0" python-versions = "^3.8.0" -content-hash = "74594958b759677bf893d1496c7430ecc0d4afdfb77adeaf85ef6358497773b9" +content-hash = "ec95407cfb86571236a1491ab076f5ffff0fc031305afde95f0d9fb198e1851b" diff --git a/pyproject.toml b/pyproject.toml index cfec5ead..d6076233 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,7 @@ pynetdicom = "^2.0.2" requests = "^2.25.1" rt-utils = "^1.1.4" matplotlib = "^3.2.2" -pandas = "^1.3.0" +pandas = "^2.0.3" vtk = { version = "^9.1.0", optional = true } nnunet = { version = "^1.7.0", optional = true } @@ -41,7 +41,7 @@ psutil = { version = "^5.8.0", optional = true } gunicorn = { version = "^20.0.4", optional = true } Jinja2 = { version = "^3.1", optional = true } pymedphys = { version = ">=0.38.0", optional = true } - + [tool.poetry.extras] cardiac = ["vtk", "nnunet"] @@ -55,7 +55,7 @@ backend = [ "psutil", "gunicorn", "Jinja2", - "pymedphys" + "pymedphys", ] [tool.poetry.group.dev.dependencies] @@ -67,6 +67,7 @@ jupyterlab = "^3.0.17" nbstripout = "^0.3.9" watchdog = "^2.0.2" argh = "^0.26.2" +ipykernel = "^6.25.1" [tool.poetry.group.docs.dependencies] sphinx = "^5.1.1" From 521114573ee0a561238dc6a69b39385d771494dc Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Mon, 14 Aug 2023 13:08:29 +1000 Subject: [PATCH 14/32] Update cmap function in example notebooks --- examples/dvh_analysis.ipynb | 9 +++++---- examples/visualise.ipynb | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/examples/dvh_analysis.ipynb b/examples/dvh_analysis.ipynb index 1f598ed4..e6f89eff 100644 --- a/examples/dvh_analysis.ipynb +++ b/examples/dvh_analysis.ipynb @@ -23,6 +23,7 @@ " !pip install platipy\n", " import platipy\n", "\n", + "import matplotlib\n", "import matplotlib.pyplot as plt\n", "import SimpleITK as sitk\n", "\n", @@ -103,7 +104,7 @@ "source": [ "vis = ImageVisualiser(ct_image, cut=get_com(structures[\"PTV60\"]))\n", "\n", - "vis.add_scalar_overlay(dose, discrete_levels=20, colormap=plt.cm.get_cmap(\"inferno\"), name=\"Dose (Gy)\")\n", + "vis.add_scalar_overlay(dose, discrete_levels=20, colormap=matplotlib.colormaps.get_cmap(\"inferno\"), name=\"Dose (Gy)\")\n", "vis.add_contour(structures)\n", "\n", "fig = vis.show()" @@ -160,7 +161,7 @@ "\n", "# Plot the DVH\n", "fig, ax = plt.subplots()\n", - "plt_dvh.plot(ax=ax, kind=\"line\", colormap=plt.cm.get_cmap(\"rainbow\"), legend=False)\n", + "plt_dvh.plot(ax=ax, kind=\"line\", colormap=matplotlib.colormaps.get_cmap(\"rainbow\"), legend=False)\n", "\n", "# Add labels and show plot\n", "plt.legend(loc='best')\n", @@ -226,8 +227,8 @@ " d_cc_points=[10],\n", " structure_for_limits=dose>5,\n", " expansion_for_limits=40,\n", - " contour_cmap=plt.cm.get_cmap(\"rainbow\"),\n", - " dose_cmap=plt.cm.get_cmap(\"inferno\"),\n", + " contour_cmap=matplotlib.colormaps.get_cmap(\"rainbow\"),\n", + " dose_cmap=matplotlib.colormaps.get_cmap(\"inferno\"),\n", " title=\"TCGA_CV_5977 Dose Metrics\")" ] }, diff --git a/examples/visualise.ipynb b/examples/visualise.ipynb index 5c78fe8b..df3a78bc 100644 --- a/examples/visualise.ipynb +++ b/examples/visualise.ipynb @@ -32,10 +32,11 @@ "# Function to grab some test data\n", "from platipy.imaging.tests.data import get_lung_nifti\n", "\n", - "# Usual suspects\n", + "# Import some common libraries which we need\n", "import numpy as np\n", "import SimpleITK as sitk\n", "from pathlib import Path\n", + "import matplotlib\n", "import matplotlib.pyplot as plt\n", "\n", "# Some utilities we use for generating interesting data\n", @@ -153,7 +154,7 @@ "metadata": {}, "outputs": [], "source": [ - "image_visualiser = ImageVisualiser(ct_image, window=(-900, 1100), colormap=plt.cm.get_cmap(\"terrain\"), figure_size_in=6)\n", + "image_visualiser = ImageVisualiser(ct_image, window=(-900, 1100), colormap=matplotlib.colormaps.get_cmap(\"terrain\"), figure_size_in=6)\n", "\n", "image_visualiser.set_limits_from_label(contours[\"LUNG_L\"] + contours[\"LUNG_R\"])\n", "\n", @@ -238,7 +239,7 @@ "image_visualiser.add_vector_overlay(\n", " dvf_expansion,\n", " name=\"DVF magnitude [mm]\",\n", - " colormap=plt.cm.get_cmap(\"gnuplot2\"),\n", + " colormap=matplotlib.colormaps.get_cmap(\"gnuplot2\"),\n", " alpha=0.75,\n", " arrow_scale=1,\n", " arrow_width=1,\n", @@ -314,7 +315,7 @@ "image_visualiser.add_vector_overlay(\n", " dvf_expansion,\n", " name=\"DVF magnitude [mm]\",\n", - " colormap=plt.cm.get_cmap(\"gnuplot2\"),\n", + " colormap=matplotlib.colormaps.get_cmap(\"gnuplot2\"),\n", " alpha=0.5,\n", " arrow_scale=1,\n", " arrow_width=1,\n", From 27ab36a6a4c10019282379cb41b87fcf825ef6fe Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Mon, 14 Aug 2023 15:22:53 +1000 Subject: [PATCH 15/32] Add total segmentator service --- .github/workflows/package.yml | 10 ++ services/totalsegmentator/Dockerfile | 14 +++ .../requirements-totalseg.txt | 4 + services/totalsegmentator/service.py | 95 +++++++++++++++++++ 4 files changed, 123 insertions(+) create mode 100644 services/totalsegmentator/Dockerfile create mode 100644 services/totalsegmentator/requirements-totalseg.txt create mode 100644 services/totalsegmentator/service.py diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index 5d475d08..ec941954 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -124,3 +124,13 @@ jobs: tags: | platipy/platipy:nnunet ghcr.io/pyplati/platipy:nnunet + + - name: Build and Push TotalSegmentator Image + uses: docker/build-push-action@v2 + with: + context: services/totalsegmentator + platforms: linux/amd64 + push: true + tags: | + platipy/platipy:totalsegmentator + ghcr.io/pyplati/platipy:totalsegmentator diff --git a/services/totalsegmentator/Dockerfile b/services/totalsegmentator/Dockerfile new file mode 100644 index 00000000..b21a3c8a --- /dev/null +++ b/services/totalsegmentator/Dockerfile @@ -0,0 +1,14 @@ +FROM platipy/platipy:service + +RUN env -C /platipy /root/.local/bin/poetry install -E backend + +COPY . /home/service + +ENV FLASK_APP service.py + +RUN pip install -r requirements-totalseg.txt + +COPY . . + +RUN download_pretrained_weights + diff --git a/services/totalsegmentator/requirements-totalseg.txt b/services/totalsegmentator/requirements-totalseg.txt new file mode 100644 index 00000000..d0719fed --- /dev/null +++ b/services/totalsegmentator/requirements-totalseg.txt @@ -0,0 +1,4 @@ +TotalSegmentator +torch +torchvision +torchaudio diff --git a/services/totalsegmentator/service.py b/services/totalsegmentator/service.py new file mode 100644 index 00000000..385c9fe8 --- /dev/null +++ b/services/totalsegmentator/service.py @@ -0,0 +1,95 @@ +# Copyright 2021 University of New South Wales, University of Sydney, Ingham Institute + +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at + +# http://www.apache.org/licenses/LICENSE-2.0 + +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +import os +import subprocess + +from pathlib import Path + +import logging +import SimpleITK as sitk + +from totalsegmentator.python_api import totalsegmentator + +from platipy.backend import app, DataObject, celery # pylint: disable=unused-import + +logger = logging.getLogger(__name__) + +TOTALSEG_SETTINGS_DEFAULTS = { + "fast": False, + "body_seg": False, +} + + +@app.register("TotalSegmentator Service", default_settings=TOTALSEG_SETTINGS_DEFAULTS) +def totalsegmentator_service(data_objects, working_dir, settings): + """ + Run the TotalSegmentator + """ + + output_objects = [] + + logger.info("Running TotalSegmentator") + logger.info("Using settings: %s", settings) + logger.info("Working Dir: %s", working_dir) + + input_path = Path(working_dir).joinpath("input") + input_path.mkdir() + + output_path = Path(working_dir).joinpath("output") + output_path.mkdir() + + for data_object in data_objects: + # Create a symbolic link for each image to auto-segment using the nnUNet + do_path = Path(data_object.path) + io_path = input_path.joinpath("image_0000.nii.gz") + load_path = data_object.path + if data_object.type == "DICOM": + load_path = sitk.ImageSeriesReader().GetGDCMSeriesFileNames(do_path) + + img = sitk.ReadImage(load_path) + sitk.WriteImage(img, str(io_path)) + + logger.info("Running TotalSegmentator on input path: %s", input_path) + totalsegmentator( + input_path, + output_path, + fast=default_settings["fast"], + body_seg=default_settings["body_seg"], + ) + + for op in output_path.glob("*.nii.gz"): + output_data_object = DataObject(type="FILE", path=str(op), parent=data_object) + output_objects.append(output_data_object) + + os.remove(io_path) + + logger.info("Finished running TotalSegmentator") + + return output_objects + + +if __name__ == "__main__": + # Run app by calling "python service.py" from the command line + + DICOM_LISTENER_PORT = 7777 + DICOM_LISTENER_AETITLE = "NNUNET_EXPORT_SERVICE" + + app.run( + debug=True, + host="0.0.0.0", + port=8001, + dicom_listener_port=DICOM_LISTENER_PORT, + dicom_listener_aetitle=DICOM_LISTENER_AETITLE, + ) From b542c477ad42339b4b9d95c5fead717e3cd17277 Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Mon, 14 Aug 2023 16:07:25 +1000 Subject: [PATCH 16/32] Corrections to Dockerfile --- services/totalsegmentator/Dockerfile | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/services/totalsegmentator/Dockerfile b/services/totalsegmentator/Dockerfile index b21a3c8a..847f3d24 100644 --- a/services/totalsegmentator/Dockerfile +++ b/services/totalsegmentator/Dockerfile @@ -1,8 +1,6 @@ FROM platipy/platipy:service -RUN env -C /platipy /root/.local/bin/poetry install -E backend - -COPY . /home/service +COPY requirements-totalseg.txt requirements-totalseg.txt ENV FLASK_APP service.py @@ -10,5 +8,6 @@ RUN pip install -r requirements-totalseg.txt COPY . . -RUN download_pretrained_weights +ENV TOTALSEG_DISABLE_HTTP1=1 +RUN totalseg_download_weights From e57e2beb61a8fdf67cf1d36f05aecac5671733df Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Tue, 15 Aug 2023 11:03:26 +1000 Subject: [PATCH 17/32] Fixes to total segmentator service --- services/radiomics/service.py | 9 +----- services/totalsegmentator/Dockerfile | 42 ++++++++++++++++++++++++++-- 2 files changed, 40 insertions(+), 11 deletions(-) diff --git a/services/radiomics/service.py b/services/radiomics/service.py index b9c67ad8..a21cd38d 100644 --- a/services/radiomics/service.py +++ b/services/radiomics/service.py @@ -15,6 +15,7 @@ import os import logging + logger = logging.getLogger(__name__) import SimpleITK as sitk @@ -98,10 +99,8 @@ def pyradiomics_extractor(data_objects, working_dir, settings): results = None meta_data_cols = [("", "Contour")] for data_obj in data_objects: - try: if len(data_obj.children) > 0: - logger.info("Running on data object: %s", data_obj.path) # Read the image series @@ -112,7 +111,6 @@ def pyradiomics_extractor(data_objects, working_dir, settings): # Children of Image Data Object are masks, compute PyRadiomics for all of them! output_frame = pd.DataFrame() for child_obj in data_obj.children: - contour_name = child_obj.path.split("/")[-1].split(".")[0] if len(settings["contours"]) > 0 and not contour_name in settings["contours"]: # If a contour list is provided and this contour isn't in the list then @@ -152,7 +150,6 @@ def pyradiomics_extractor(data_objects, working_dir, settings): logger.info("Computing Radiomics for contour: %s", contour_name) for rad in settings["radiomics"].keys(): - logger.info("Computing %s radiomics", rad) if rad not in AVAILABLE_RADIOMICS.keys(): @@ -192,7 +189,6 @@ def pyradiomics_extractor(data_objects, working_dir, settings): # Add the meta data for this contour if there is any if child_obj.meta_data: for key in child_obj.meta_data: - col_key = ("", key) output_frame[col_key] = child_obj.meta_data[key] @@ -203,7 +199,6 @@ def pyradiomics_extractor(data_objects, working_dir, settings): # Add Image Series Data Object's Meta Data to the table if data_obj.meta_data: for key in data_obj.meta_data.keys(): - col_key = ("", key) output_frame[col_key] = pd.Series( @@ -243,7 +238,6 @@ def pyradiomics_extractor(data_objects, working_dir, settings): class RadiomicsEndpoint(Resource): def get(self): - logger.info(firstorder.RadiomicsFirstOrder.getFeatureNames()) result = {} @@ -257,7 +251,6 @@ def get(self): api.add_resource(RadiomicsEndpoint, "/api/radiomics") if __name__ == "__main__": - # Run app by calling "python service.py" from the command line DICOM_LISTENER_PORT = 7777 diff --git a/services/totalsegmentator/Dockerfile b/services/totalsegmentator/Dockerfile index 847f3d24..ba4b8e2b 100644 --- a/services/totalsegmentator/Dockerfile +++ b/services/totalsegmentator/Dockerfile @@ -1,4 +1,10 @@ -FROM platipy/platipy:service +FROM nvidia/cuda:12.2.0-runtime-ubuntu22.04 + +RUN apt update; apt install -y python3 python3-pip + +RUN ln -s /usr/bin/python3 /usr/bin/python + +RUN pip install platipy[backend] COPY requirements-totalseg.txt requirements-totalseg.txt @@ -6,8 +12,38 @@ ENV FLASK_APP service.py RUN pip install -r requirements-totalseg.txt -COPY . . - ENV TOTALSEG_DISABLE_HTTP1=1 RUN totalseg_download_weights + +RUN apt install -y redis-server +COPY entrypoint.sh /entrypoint.sh +RUN chmod +x /entrypoint.sh + +ENV LANG C.UTF-8 +ENV LC_ALL C.UTF-8 + +ARG dicom_listen_port=7777 + +ENV DICOM_LISTEN_PORT ${dicom_listen_port} +ENV DICOM_LISTEN_AET PLATIPY_SERVICE + +RUN printf '#!/bin/bash\npython3 -m platipy.backend.manage $@\n' > /usr/bin/manage && \ + chmod +x /usr/bin/manage + +EXPOSE 8000 +EXPOSE ${dicom_listen_port} + +ENV PYTHONPATH "/home/service" +WORKDIR /home/service + +ENV WORK /data +RUN mkdir /logs /data && chmod 0777 /logs /data + +RUN pip install "SQLAlchemy<2.0.0" + +ENTRYPOINT ["/entrypoint.sh"] + +CMD [ "manage" ] + +COPY . . From 7ad82cd36a18aca0c75892e17a686e7cc617804f Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Tue, 15 Aug 2023 15:54:18 +1000 Subject: [PATCH 18/32] Add prefix for total segmentator structure names --- services/totalsegmentator/service.py | 39 +++++++++++++++++++++------- 1 file changed, 30 insertions(+), 9 deletions(-) diff --git a/services/totalsegmentator/service.py b/services/totalsegmentator/service.py index 385c9fe8..bed706b0 100644 --- a/services/totalsegmentator/service.py +++ b/services/totalsegmentator/service.py @@ -27,6 +27,7 @@ logger = logging.getLogger(__name__) TOTALSEG_SETTINGS_DEFAULTS = { + "output_prefix": "TS_", "fast": False, "body_seg": False, } @@ -52,25 +53,45 @@ def totalsegmentator_service(data_objects, working_dir, settings): for data_object in data_objects: # Create a symbolic link for each image to auto-segment using the nnUNet - do_path = Path(data_object.path) io_path = input_path.joinpath("image_0000.nii.gz") load_path = data_object.path if data_object.type == "DICOM": - load_path = sitk.ImageSeriesReader().GetGDCMSeriesFileNames(do_path) + load_path = sitk.ImageSeriesReader().GetGDCMSeriesFileNames(load_path) img = sitk.ReadImage(load_path) sitk.WriteImage(img, str(io_path)) - logger.info("Running TotalSegmentator on input path: %s", input_path) - totalsegmentator( - input_path, - output_path, - fast=default_settings["fast"], - body_seg=default_settings["body_seg"], - ) + logger.info("Running TotalSegmentator on input path: %s", str(io_path)) + + command = [ + "TotalSegmentator", + "-i", + str(io_path), + "-o", + str(output_path), + ] + + if settings["fast"]: + command += ["--fast"] + + if settings["body_seg"]: + command += ["--body_seg"] + + logger.info("Running command: %s", command) + subprocess.call(command) for op in output_path.glob("*.nii.gz"): + # Check its not empty + mask = sitk.ReadImage(str(op)) + if sitk.GetArrayFromImage(mask).sum() == 0: + logger.info("Skipping empty segmentation: %s", op.name) + continue + + # Rename the file with the prefix + new_name = f"{settings['output_prefix']}{op.name}" + op = op.rename(op.parent.joinpath(new_name)) output_data_object = DataObject(type="FILE", path=str(op), parent=data_object) + logger.info("Found segmentation file: %s", op.name) output_objects.append(output_data_object) os.remove(io_path) From d7856ba3ea9eeb7481d5110fcf4f6ab1558ca9a1 Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Tue, 15 Aug 2023 15:55:06 +1000 Subject: [PATCH 19/32] Add entrypoint file for total segmentator service --- services/totalsegmentator/entrypoint.sh | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 services/totalsegmentator/entrypoint.sh diff --git a/services/totalsegmentator/entrypoint.sh b/services/totalsegmentator/entrypoint.sh new file mode 100644 index 00000000..40f814ca --- /dev/null +++ b/services/totalsegmentator/entrypoint.sh @@ -0,0 +1,23 @@ +#!/usr/bin/env bash + +# Run redis-server +redis-server --daemonize yes + +# Run celery beat and worker +celery --app=service:celery beat --loglevel=INFO & +celery --app=service:celery worker --loglevel=INFO & + +# Start the DICOM listener for the service +celery --app=service:celery call platipy.backend.tasks.run_dicom_listener + +# Run the gunicorn server +CERT_FILE=service.crt +KEY_FILE=service.key +if [ -f "$CERT_FILE" ]; then + echo "SSL Certificates Found. Will serve over HTTPS." + exec gunicorn -b :8000 --certfile=service.crt --keyfile=service.key --timeout 300 --graceful-timeout 60 --access-logfile - --error-logfile - service:app +else + echo "WARNING: No SSL certificates found. Generate them with 'manage ssl'." + echo "Running without SSL, not suitable for production use." + exec gunicorn -b :8000 --timeout 300 --graceful-timeout 60 --access-logfile - --error-logfile - service:app +fi From d11d26ee7145fc84946452965ea4b131855d762d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 30 Aug 2023 00:21:04 +0000 Subject: [PATCH 20/32] Bump jupyter-server from 2.7.0 to 2.7.2 Bumps [jupyter-server](https://github.com/jupyter-server/jupyter_server) from 2.7.0 to 2.7.2. - [Release notes](https://github.com/jupyter-server/jupyter_server/releases) - [Changelog](https://github.com/jupyter-server/jupyter_server/blob/main/CHANGELOG.md) - [Commits](https://github.com/jupyter-server/jupyter_server/compare/v2.7.0...v2.7.2) --- updated-dependencies: - dependency-name: jupyter-server dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 69 +++++++++++++++++------------------------------------ 1 file changed, 22 insertions(+), 47 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8fd82f81..cf5f588e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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registration.SetMetricSamplingPercentage(sampling_rate, seed=42) registration.SetMetricSamplingStrategy(sitk.ImageRegistrationMethod.REGULAR) # This is only necessary if using a transform comprising changes with different units From 17f604139c35b1b97ba099073fb7cd86eca29c07 Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Mon, 25 Sep 2023 09:07:04 +1000 Subject: [PATCH 22/32] Adjust casts for Mask Negated image filter --- platipy/imaging/label/utils.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/platipy/imaging/label/utils.py b/platipy/imaging/label/utils.py index 35f8d64a..6cafffd7 100644 --- a/platipy/imaging/label/utils.py +++ b/platipy/imaging/label/utils.py @@ -168,7 +168,13 @@ def prime_encode_structure_list(structure_list): # Multiply with the encoded image prime_encoded_image = ( - sitk.MaskNegated(prime_encoded_image, s_img_int) + sitk.Cast( + sitk.MaskNegated( + sitk.Cast(prime_encoded_image, sitk.sitkUInt8), + sitk.Cast(s_img_int, sitk.sitkUInt8), + ), + sitk.sitkUInt64, + ) + sitk.Mask(prime_encoded_image, s_img_int) * prime * s_img_int ) @@ -262,7 +268,6 @@ def binary_decode_image(binary_encoded_img): num_nonzero_voxels = 1 for power in range(32): - # Calculate the region originally defined with this prime s_arr = np.bitwise_and(binary_encoded_arr, 2 ** (power + 1)) From 8d617eb0963760b69651a6c27491ecc0d96296a7 Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Mon, 25 Sep 2023 09:25:51 +1000 Subject: [PATCH 23/32] Add another cast --- platipy/imaging/label/utils.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/platipy/imaging/label/utils.py b/platipy/imaging/label/utils.py index 6cafffd7..f3e8138f 100644 --- a/platipy/imaging/label/utils.py +++ b/platipy/imaging/label/utils.py @@ -175,7 +175,9 @@ def prime_encode_structure_list(structure_list): ), sitk.sitkUInt64, ) - + sitk.Mask(prime_encoded_image, s_img_int) * prime * s_img_int + + sitk.Mask(prime_encoded_image, sitk.Cast(s_img_int, sitk.sitkUInt8)) + * prime + * s_img_int ) return prime_encoded_image From 196f57336c70a85525f516e673c35a13dacf00ce Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Mon, 25 Sep 2023 09:36:04 +1000 Subject: [PATCH 24/32] Remove stray print statement --- platipy/imaging/registration/deformable.py | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/platipy/imaging/registration/deformable.py b/platipy/imaging/registration/deformable.py index ced1d60c..39231c9d 100644 --- a/platipy/imaging/registration/deformable.py +++ b/platipy/imaging/registration/deformable.py @@ -65,7 +65,6 @@ def multiscale_demons( moving_images = [] for resolution, smoothing_sigma in zip(resolution_staging, smoothing_sigmas): - isotropic_voxel_size_mm = None shrink_factor = None @@ -123,9 +122,7 @@ def multiscale_demons( ) initial_displacement_field.CopyInformation(fixed_image) else: - initial_displacement_field = sitk.Resample( - initial_displacement_field, fixed_image - ) + 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00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 3 Oct 2023 00:17:19 +0000 Subject: [PATCH 25/32] Bump urllib3 from 2.0.4 to 2.0.6 Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.4 to 2.0.6. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/2.0.4...2.0.6) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... 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[Commits](https://github.com/urllib3/urllib3/compare/2.0.6...2.0.7) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 0673ca89..55e19082 100644 --- a/poetry.lock +++ b/poetry.lock @@ -4559,13 +4559,13 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake [[package]] name = "urllib3" -version = "2.0.6" +version = "2.0.7" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.7" files = [ - {file = "urllib3-2.0.6-py3-none-any.whl", hash = "sha256:7a7c7003b000adf9e7ca2a377c9688bbc54ed41b985789ed576570342a375cd2"}, - {file = "urllib3-2.0.6.tar.gz", hash = "sha256:b19e1a85d206b56d7df1d5e683df4a7725252a964e3993648dd0fb5a1c157564"}, + {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"}, + {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"}, ] [package.extras] From 22cfe5cad197e3efdb7149e11acc108cfb2b0fb9 Mon Sep 17 00:00:00 2001 From: Phillip Chlap Date: Tue, 7 Nov 2023 09:20:11 +1300 Subject: [PATCH 28/32] Replace hardcoded interpolator values --- platipy/imaging/registration/deformable.py | 6 +++--- platipy/imaging/visualisation/utils.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/platipy/imaging/registration/deformable.py b/platipy/imaging/registration/deformable.py index 39231c9d..2ce18054 100644 --- a/platipy/imaging/registration/deformable.py +++ b/platipy/imaging/registration/deformable.py @@ -199,7 +199,7 @@ def fast_symmetric_forces_demons_registration( smoothing_sigmas=False, default_value=None, ncores=1, - interp_order=2, + interp_order=sitk.sitkLinear, verbose=False, ): """ @@ -318,7 +318,7 @@ def bspline_registration( metric="mean_squares", initial_grid_spacing=64, grid_scale_factors=[1, 2, 4], - interp_order=3, + interp_order=sitk.sitkBSpline, default_value=-1000, number_of_iterations=20, isotropic_resample=False, @@ -370,7 +370,7 @@ def bspline_registration( multiresolution stage. Defaults to [1, 2, 4]. interp_order (int, optional): Interpolation order of final resampling. - Defaults to 3 (cubic). + Defaults to sitk.sitkBSpline (cubic). default_value (int, optional): Default image value. Defaults to -1000. number_of_iterations (int, optional): Number of iterations at each resolution stage. 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