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update devel
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| """ | ||
| Code to display orthogonal image slices with crosshairs displaying the slice position | ||
| """ | ||
|
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| import numpy as np | ||
| import SimpleITK as sitk | ||
| import matplotlib.pyplot as plt | ||
|
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| """ | ||
| Settings | ||
| Fill out this section | ||
| """ | ||
|
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| # Define the image | ||
| im = sitk.ReadImage('/home/robbie/Work/4_Software/platipy/platipy/imaging/tests/data/dynamic/lung/LCTSC-Train-S1-001/CT.nii.gz') | ||
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| # Define the cut location - this is where the crosshairs will appear | ||
| # Given as [axial, coronal, sagittal] location | ||
| cut = [30, 220, 330] | ||
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| # Define the figure size (inches), colormap, intensity windowing ([min, range]) | ||
| figSize=6 | ||
| cmap=plt.cm.Greys_r | ||
| window=[-250, 500] | ||
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| # Output file name | ||
| fig_name = './test.png' | ||
|
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| """ | ||
| Code - shouldn't need to edit this | ||
| """ | ||
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| def returnSlice(axis, index): | ||
| if axis == "x": | ||
| s = (slice(None), slice(None), index) | ||
| if axis == "y": | ||
| s = (slice(None), index, slice(None)) | ||
| if axis == "z": | ||
| s = (index, slice(None), slice(None)) | ||
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| return s | ||
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| nda = sitk.GetArrayFromImage(im) | ||
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| # Get data for correct visualisation | ||
| (AxSize, CorSize, SagSize) = nda.shape | ||
| spPlane, _, spSlice = im.GetSpacing() | ||
| asp = (1.0 * spSlice) / spPlane | ||
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||
|
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| # Set up figure | ||
| fSize = ( | ||
| figSize, | ||
| figSize * (asp * AxSize + CorSize) / (1.0 * SagSize + CorSize), | ||
| ) | ||
|
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| fig, ((axAx, blank), (axCor, axSag)) = plt.subplots( | ||
| 2, | ||
| 2, | ||
| figsize=fSize, | ||
| gridspec_kw={"height_ratios": [(CorSize) / (asp * AxSize), 1], "width_ratios": [SagSize, CorSize]}, | ||
| ); | ||
| blank.axis("off") | ||
|
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| # Get slices | ||
| sAx = returnSlice("z", cut[0]) | ||
| sCor = returnSlice("y", cut[1]) | ||
| sSag = returnSlice("x", cut[2]) | ||
|
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| # Display image data | ||
| imAx = axAx.imshow( | ||
| nda.__getitem__(sAx), | ||
| aspect=1.0, | ||
| interpolation=None, | ||
| cmap=cmap, | ||
| clim=(window[0], window[0] + window[1]), | ||
| ) | ||
| imCor = axCor.imshow( | ||
| nda.__getitem__(sCor), | ||
| origin="lower", | ||
| aspect=asp, | ||
| interpolation=None, | ||
| cmap=cmap, | ||
| clim=(window[0], window[0] + window[1]), | ||
| ) | ||
| imSag = axSag.imshow( | ||
| nda.__getitem__(sSag), | ||
| origin="lower", | ||
| aspect=asp, | ||
| interpolation=None, | ||
| cmap=cmap, | ||
| clim=(window[0], window[0] + window[1]), | ||
| ) | ||
|
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| # Display crosshairs | ||
| # Axial image, FAKE cut (just for label) | ||
| axAx.plot([0, 0], [0, 0], c='yellow', label=f'Axial slice: {cut[0]}') | ||
| # Axial image, coronal cut | ||
| axAx.plot([0, SagSize], [cut[1], cut[1]], c='r', label=f'Coronal slice: {cut[1]}') | ||
| # Axial image, sagittal cut | ||
| axAx.plot([cut[2], cut[2]], [0, CorSize], c='orange', label=f'Sagittal slice: {cut[2]}') | ||
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| axAx.legend(loc='center left', bbox_to_anchor=(1.05,0.5)) | ||
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| # Sag image, ax cut | ||
| axSag.plot([0, CorSize], [cut[0], cut[0]], c='yellow') | ||
| # Sag image, cor cut | ||
| axSag.plot([cut[1], cut[1]], [0, AxSize], c='r') | ||
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| # Cor image, ax cut | ||
| axCor.plot([0, SagSize], [cut[0], cut[0]], c='yellow') | ||
| # Cor image, sagittal cut | ||
| axCor.plot([cut[2], cut[2]], [0, AxSize], c='orange') | ||
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| # Turn off axes | ||
| axAx.axis("off") | ||
| axCor.axis("off") | ||
| axSag.axis("off") | ||
|
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| # Adjust spacing | ||
| fig.subplots_adjust(left=0, right=1, wspace=0.01, hspace=0.01, top=1, bottom=0) | ||
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| # Save image | ||
| #fig.savefig(f'{fig_name}', dpi=300, transparent=True) |