Merge branch 'hotfix'

Author: crousseau

ClearMap.yml

@@ -31,5 +31,6 @@ dependencies:
   - scikit-learn
   - graph-tool
   - pytorch
+  - mkl<2024.1  # Breaks pytorch (https://github.com/pytorch/pytorch/issues/123097)
   - pip:
     - lxml

ClearMap/ImageProcessing/Binary/Smoothing.py

@@ -340,7 +340,7 @@ def smooth_by_configuration_block(source, iterations = 1, verbose = False):
   Returns
   -------
   smoothed : array
-    Thre smoothed binary array.
+    The smoothed binary array.
   """
   try:
     if isinstance(source, io.src.Source):
@@ -360,8 +360,9 @@ def smooth_by_configuration_block(source, iterations = 1, verbose = False):
       smoothed = lut[smoothed];
 
       if verbose:
-        print(f'Binary Smoothing: itertion {i+1} / {iterations} done!', flush=True)
+        print(f'Binary Smoothing: iteration {i+1} / {iterations} done!', flush=True)
   except Exception as err:
+    print(f"ERROR in smooth_by_configuration")
     print(err, flush=True)
     raise
 

ClearMap/processors/generic_tab_processor.py

@@ -1,5 +1,6 @@
 import os
 import sys
+import warnings
 from concurrent.futures.process import BrokenProcessPool
 
 
@@ -33,6 +34,7 @@ def remove_next_steps_files(self, target_step_name):
         for step_name in self.get_next_steps(target_step_name):
             f_path = self.path_from_step_name(step_name)
             if os.path.exists(f_path):
+                warnings.warn(f"WARNING: Remove previous step {step_name}, file {f_path}")
                 os.remove(f_path)
 
     def path(self, step, step_back=False, n_before=0):

ClearMap/processors/tube_map.py

@@ -205,7 +205,7 @@ def _binarize(self, n_processes, clip_range, deconvolve_threshold, channel):
         postfix = channel if channel == 'arteries' else None
         self.steps[channel].remove_next_steps_files(self.steps[channel].binary)
 
-        source = self.workspace.filename('stitched', postfix=postfix)
+        source = self.workspace.source('stitched', postfix=postfix)
         sink = self.workspace.filename('binary', postfix=postfix)
 
         binarization_parameter = copy.deepcopy(vasculature.default_binarization_parameter)
@@ -242,7 +242,7 @@ def smooth(self, channel):
 
         self.steps[channel].remove_next_steps_files(self.steps[channel].postprocessed)
 
-        source = self.workspace.filename('binary', postfix=postfix)
+        source = self.workspace.source('binary', postfix=postfix)
         sink_postfix = f'{postfix}_postprocessed' if postfix else 'postprocessed'
         sink = self.workspace.filename('binary', postfix=sink_postfix)
         sink = initialize_sink(sink, shape=source.shape, dtype=source.dtype, order=source.order,
@@ -340,7 +340,7 @@ def plot_combined(self, parent=None, arrange=False):  # TODO: final or not optio
     def combine_binary(self):
         # MERGE
         sink = self.workspace.filename('binary', postfix='combined')  # Temporary
-        if not self.processing_config['binarization']['arteries']['binarization']['run']:
+        if self.processing_config['binarization']['arteries']['binarization']['run']:
             source = self.workspace.filename('binary', postfix='filled')
             source_arteries = self.workspace.filename('binary', postfix='arteries_filled')
             block_processing.process(np.logical_or, [source, source_arteries], sink,
@@ -494,7 +494,7 @@ def skeletonize_and_build_graph(self):
         self.processing_config.reload()
         graph_cfg = self.processing_config['graph_construction']
         self.skeletonize(self.workspace.filename('skeleton'))# WARNING: main thread (prange)
-        if graph_cfg['build'] or graph_cfg['skeletonize']:
+        if graph_cfg['build']:
             self._build_graph_from_skeleton()  # WARNING: main thread (prange)
 
     def clean_graph(self):

ClearMapUi.yml

@@ -37,6 +37,7 @@ dependencies:
   - scikit-learn
   - graph-tool<=2.45  # Cannot remove self loops with later versions
   - pytorch<=1.11
+  - mkl<2024.1  # Breaks pytorch (https://github.com/pytorch/pytorch/issues/123097)
   - cudatoolkit=11.6
   - configobj
   - natsort

ClearMapUi39.yml

@@ -37,6 +37,7 @@ dependencies:
   - scikit-learn
   - graph-tool<=2.45  # Cannot remove self loops with later versions
   - pytorch<=1.11  # could probably upgrade
+  - mkl<2024.1  # Breaks pytorch (https://github.com/pytorch/pytorch/issues/123097)
   - cudatoolkit=11.6
   - configobj
   - natsort