From 84ae72d4ce6dba1b90c3347b2708e160baf8f2f0 Mon Sep 17 00:00:00 2001 From: jluethi Date: Fri, 19 Jul 2024 11:55:51 +0200 Subject: [PATCH] Refactor well position calculation into utils function --- src/napari_ome_zarr_navigator/img_browser.py | 82 ++++++++------------ src/napari_ome_zarr_navigator/roi_loader.py | 4 + src/napari_ome_zarr_navigator/util.py | 30 ++++++- 3 files changed, 63 insertions(+), 53 deletions(-) diff --git a/src/napari_ome_zarr_navigator/img_browser.py b/src/napari_ome_zarr_navigator/img_browser.py index 8632300..41b8697 100644 --- a/src/napari_ome_zarr_navigator/img_browser.py +++ b/src/napari_ome_zarr_navigator/img_browser.py @@ -1,26 +1,15 @@ -from typing import TYPE_CHECKING -import napari - -import numpy as np -import pandas as pd +import logging +import re from pathlib import Path from typing import Union -from zarr.errors import PathNotFoundError + import anndata as ad +import napari +import numpy as np +import pandas as pd import zarr -import dask.array as da -import re -import logging - - -from napari_ome_zarr_navigator.util import alpha_to_numeric -from napari_ome_zarr_navigator.roi_loader import ROILoaderPlate - # from fractal_tasks_core.roi import convert_ROI_table_to_indices -from fractal_tasks_core.ngff import load_NgffImageMeta -from fractal_tasks_core.ngff.zarr_utils import load_NgffPlateMeta - from magicgui.widgets import ( CheckBox, ComboBox, @@ -29,6 +18,13 @@ PushButton, Select, ) +from zarr.errors import PathNotFoundError + +from napari_ome_zarr_navigator.roi_loader import ROILoaderPlate +from napari_ome_zarr_navigator.util import ( + alpha_to_numeric, + calculate_well_positions, +) logger = logging.getLogger(__name__) logging.getLogger("ome_zarr").setLevel(logging.WARN) @@ -78,14 +74,16 @@ def initialize_filters(self): Container( widgets=[ ComboBox( - choices=sorted(self.df[filter].unique()), + choices=sorted( + self.df[filter_name].unique() + ), enabled=False, ), - CheckBox(label=filter, value=False), + CheckBox(label=filter_name, value=False), ], layout="horizontal", ) - for filter in self.filter_names + for filter_name in self.filter_names ], layout="vertical", ) @@ -189,52 +187,34 @@ def load_roi(self): ) def go_to_well(self): - # TODO: deativate go to if only a single plate is loaded - matches = [ re.match(r"([A-Z]+)(\d+)", well) for well in self.well.value ] wells = [(m.group(1), m.group(2)) for m in matches] - dataset = 0 - level = 0 - zarr_url = f"{self.zarr_root}/{wells[0][0]}/{wells[0][1]}/{dataset}" - shape = da.from_zarr(f"{zarr_url}/{level}").shape[-2:] - image_meta = load_NgffImageMeta(zarr_url) - scale = image_meta.get_pixel_sizes_zyx(level=level)[-2:] - plate_meta = load_NgffPlateMeta(self.zarr_root) - rows = [x.name for x in plate_meta.plate.rows] - cols = [x.name for x in plate_meta.plate.columns] for layer in self.viewer.layers: - if type(layer) == napari.layers.Shapes: + if type(layer) == napari.layers.Shapes and re.match( + r"([A-Z]+)(\d+)", layer.name + ): self.viewer.layers.remove(layer) - for row_alpha, col_str in wells: - row = rows.index(row_alpha) - col = cols.index(col_str) - - rec = np.array( - [ - [row * scale[0] * shape[0], col * scale[1] * shape[1]], - [ - (row + 1) * scale[0] * shape[0], - (col + 1) * scale[1] * shape[1], - ], - ] + for well in wells: + top_left_corner, bottom_right_corner = calculate_well_positions( + plate_url=self.zarr_root, row=well[0], col=well[1] ) - + rec = np.array([top_left_corner, bottom_right_corner]) self.viewer.add_shapes( rec, shape_type="rectangle", edge_width=10, edge_color="white", face_color="transparent", - name=f"{row_alpha}{col_str}", + name=f"{well[0]}{well[1]}", ) - self.viewer.camera.center = rec.mean(axis=0) - self.viewer.camera.zoom = 0.25 + self.viewer.camera.center = rec.mean(axis=0) + self.viewer.camera.zoom = 0.25 def parse_zarr_url(zarr_url: Union[str, Path]) -> dict: @@ -293,7 +273,7 @@ def load_table( """ wells = _validate_wells(wells, zarr_url) wells_str = [f"{w[0]}{w[1]}" for w in wells] - tbl = list() + tbl = [] while wells: row_alpha, col = wells.pop() try: @@ -328,12 +308,12 @@ def _validate_wells( if wells is not None: wells = [wells] if isinstance(wells, str) else wells matches = [re.match(r"([A-Z]+)(\d+)", well) for well in wells] - wells = set([(m.group(1), m.group(2)) for m in matches]) + wells = {(m.group(1), m.group(2)) for m in matches} else: with zarr.open(zarr_url) as metadata: matches = [ re.match(r"([A-Z]+)/(\d+)", well["path"]) for well in metadata.attrs["plate"]["wells"] ] - wells = set([(m.group(1), m.group(2)) for m in matches]) + wells = {(m.group(1), m.group(2)) for m in matches} return wells diff --git a/src/napari_ome_zarr_navigator/roi_loader.py b/src/napari_ome_zarr_navigator/roi_loader.py index 1c41a91..5b6a32f 100644 --- a/src/napari_ome_zarr_navigator/roi_loader.py +++ b/src/napari_ome_zarr_navigator/roi_loader.py @@ -364,6 +364,10 @@ def __init__( self._zarr_picker.choices = zarr_images self._zarr_picker._default_choices = zarr_images + # TODO: Calculate base translation for a given well + # Needs top-left corner of the well + self.translation = 1 + # # Handle defaults for plate loading # if "well_ROI_table" in self._roi_table_picker.choices: # self._roi_table_picker.value = "well_ROI_table" diff --git a/src/napari_ome_zarr_navigator/util.py b/src/napari_ome_zarr_navigator/util.py index 4b38b8a..f96676c 100644 --- a/src/napari_ome_zarr_navigator/util.py +++ b/src/napari_ome_zarr_navigator/util.py @@ -1,9 +1,12 @@ #!/usr/bin/env python3 import string + +import anndata as ad +import dask.array as da import napari +from fractal_tasks_core.ngff import load_NgffImageMeta +from fractal_tasks_core.ngff.zarr_utils import load_NgffPlateMeta from zarr.errors import PathNotFoundError -import anndata as ad -import pandas as pd def alpha_to_numeric(alpha: str) -> int: @@ -51,3 +54,26 @@ def add_features_to_labels( labels_layer.predictions = ann_tbl.obs except PathNotFoundError: pass + + +def calculate_well_positions(plate_url, row, col): + dataset = 0 + level = 0 + zarr_url = f"{plate_url}/{row}/{col}/{dataset}" + shape = da.from_zarr(f"{zarr_url}/{level}").shape[-2:] + image_meta = load_NgffImageMeta(zarr_url) + scale = image_meta.get_pixel_sizes_zyx(level=level)[-2:] + plate_meta = load_NgffPlateMeta(plate_url) + rows = [x.name for x in plate_meta.plate.rows] + cols = [x.name for x in plate_meta.plate.columns] + + row = rows.index(row) + col = cols.index(col) + + top_left_corner = [row * scale[0] * shape[0], col * scale[1] * shape[1]] + bottom_right_corner = [ + (row + 1) * scale[0] * shape[0], + (col + 1) * scale[1] * shape[1], + ] + + return top_left_corner, bottom_right_corner