Exported single-channel TIFs for purposes of ilastik classifier development

extensions/chaeo/actual_runs/20230805_kristineberg_PA.py

@@ -3,6 +3,19 @@ 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
+
+def export_single_channel_tif_from_multichannel_czi(files, where_output, channel):
+
+    for czif in files:
+        in_acc = CziImageFileAccessor(czif)
+        outf = Path(where_output) / (Path(czif).stem + '.tif')
+        write_accessor_data_to_file(
+            outf,
+            in_acc.get_one_channel_data(channel),
+        )
+        print(f'Wrote file: {outf}')
+
 if __name__ == '__main__':
     where_czi = 'c:/Users/rhodes/projects/proj0012-trec-handoff/owncloud-sync/TREC-HD/Images/TREC_STOP_15_Kristineberg/230805_automic_AI_PA/20230805-122525_AI_PA_successfulrun_recognitiononPLL405cilindionas/Selection'
     where_output = autonumber_new_directory(
@@ -17,7 +30,7 @@ if __name__ == '__main__':
         'pxmap_threshold': 0.25,
         'pixel_class': 0,
         'zmask_channel': 0,
-        'patches_channel': 4,
+        'patches_channel': 2,
         'mask_type': 'boxes',
         'zmask_filters': {'area': (1e3, 1e8)},
         'zmask_expand_box_by': (128, 3),
@@ -31,12 +44,18 @@ if __name__ == '__main__':
 
     input_files = get_matching_files(where_czi, 'czi')
 
-    loop_workflow(
-        input_files,
-        where_output,
-        export_patches_from_multichannel_zstack,
-        params,
-        catch_and_continue=False,
-    )
+    tif_export_params = {
+        'channel': 0
+    }
+
+    export_single_channel_tif_from_multichannel_czi(input_files, where_output, 0)
+
+    # loop_workflow(
+    #     input_files,
+    #     where_output,
+    #     export_single_channel_tif_from_multichannel_czi,
+    #     tif_export_params,
+    #     catch_and_continue=False,
+    # )
 
     print('Finished')
\ No newline at end of file

extensions/chaeo/util.py

@@ -26,7 +26,7 @@ def autonumber_new_file(where: str, prefix: str, ext: str) -> str:
             idx = max(idx, int(ma.groups()[0]) + 1)
     return f'{prefix}-{idx:04d}.{ext}'
 
-def get_matching_files(where: str, ext: str, coord_filter: dict={}) -> str:
+def get_matching_files(where: str, ext: str, coord_filter: dict={}) -> list:
     files = []
 
     def is_filtered_out(ff):
@@ -54,7 +54,7 @@ def loop_workflow(files, where_output, workflow_func, params,
     failures = []
     for ii, ff in enumerate(files):
         export_kwargs = {
-            'input_zstack_path': ff,
+            'input_zstack_path': ff,  # TODO: use a more generic name for implied args
             'where_output': where_output,
             **params,
         }