Elevate whether to use a specific z-index or MIP to find best focus in zmask

extensions/chaeo/actual_runs/20231008_Bilbao_PA.py

+from pathlib import Path
+
+from extensions.chaeo.util import autonumber_new_directory, get_matching_files, loop_workflow
+from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
+
+from model_server.accessors import CziImageFileAccessor, write_accessor_data_to_file, InMemoryDataAccessor
+from model_server.process import rescale
+
+
+def export_single_channel_tif_from_multichannel_czi(input_file_path, output_folder_path, channel, **kwargs):
+    in_acc = CziImageFileAccessor(input_file_path)
+    data = in_acc.get_one_channel_data(channel).data
+    if 'rescale_zmask_clip' in kwargs:
+        data = rescale(data, clip=kwargs['rescale_zmask_clip'])
+    outf = Path(output_folder_path) / (Path(input_file_path).stem + '.tif')
+    write_accessor_data_to_file(
+        outf,
+        InMemoryDataAccessor(data),
+    )
+    print(f'Wrote file: {outf}')
+
+if __name__ == '__main__':
+    root = Path('c:/Users/rhodes/projects/proj0012-trec-handoff/owncloud-sync/TREC-HD/Images/')
+    where_czi = (root / 'TREC_STOP_24_Bilbao/231008_automic/20231008-162336/Selection').__str__()
+    where_output = autonumber_new_directory(
+        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0017/output',
+        'batch-output'
+    )
+
+    px_ilp = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/exp0017/pxAF405_dim8bit.ilp').__str__()
+
+    params = {
+        'ilastik_project_file': px_ilp,
+        'pxmap_threshold': 0.25,
+        'pixel_class': 0,
+        'zmask_channel': 0,
+        'zmask_zindex': 3,
+        'patches_channel': 2,
+        'mask_type': 'boxes',
+        'zmask_filters': {'area': (1e3, 1e8)},
+        'zmask_expand_box_by': (128, 3),
+        'export_pixel_probabilities': True,
+        'export_2d_patches_for_training': True,
+        'draw_bounding_box_on_2d_patch': True,
+        'export_2d_patches_for_annotation': True,
+        'export_3d_patches': False,
+        'export_annotated_zstack': True,
+        'export_patch_masks': True,
+        'rescale_zmask_clip': 0.01,
+        'rgb_overlay_channels': (1, None, None),
+        'rgb_overlay_weights': (0.5, 1.0, 1.0)
+    }
+
+    input_files = get_matching_files(where_czi, 'czi', coord_filter={})
+
+    loop_workflow(
+        input_files,
+        where_output,
+        export_patches_from_multichannel_zstack,
+        params,
+        catch_and_continue=False,
+    )
+
+    print('Finished')
\ No newline at end of file

extensions/chaeo/workflows.py

@@ -23,6 +23,7 @@ def export_patches_from_multichannel_zstack(
         pxmap_threshold: float,
         pixel_class: int,
         zmask_channel: int,
+        zmask_zindex: None,  # None for MIP,
         patches_channel: int,
         rescale_zmask_clip: int = None,
         mask_type: str = 'boxes',
@@ -46,7 +47,11 @@ def export_patches_from_multichannel_zstack(
     ti.click('file_input')
 
     # MIP and classify pixels
-    zmask_data = stack.get_one_channel_data(channel=zmask_channel).data.max(axis=-1, keepdims=True)
+    if isinstance(zmask_zindex, int):
+        assert 0 < zmask_zindex < stack.nz
+        zmask_data = stack.get_one_channel_data(channel=zmask_channel).data[:, :, :, zmask_zindex]
+    else:
+        zmask_data = stack.get_one_channel_data(channel=zmask_channel).data.max(axis=-1, keepdims=True)
     if rescale_zmask_clip:
         zmask_data = rescale(zmask_data, rescale_zmask_clip)
     mip = InMemoryDataAccessor(