small-fish-gui 1.10.3__tar.gz → 1.10.4__tar.gz

{small_fish_gui-1.10.3 → small_fish_gui-1.10.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.10.3
+Version: 1.10.4
 Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
 Project-URL: Homepage, https://github.com/2Echoes/small_fish
 Project-URL: Wiki, https://github.com/2Echoes/small_fish_gui/wiki
@@ -12,6 +12,7 @@ Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.9
 Requires-Dist: aicsimageio>=4.14.0
+Requires-Dist: aicspylibczi==3.3.1
 Requires-Dist: big-fish==0.6.2
 Requires-Dist: cellpose==3.0.7
 Requires-Dist: czifile==2019.7.2

small_fish_gui-1.10.4/error_log.txt

@@ -0,0 +1,9 @@
+version 1.10.3error : 'voxel_size_z'traceback :
+Traceback (most recent call last):
+  File "/home/floric/miniconda3/envs/dev/lib/python3.9/site-packages/small_fish_gui/pipeline/main.py", line 40, in <module>
+    new_result_df, new_cell_result_df, acquisition_id, user_parameters =  add_detection(
+  File "/home/floric/miniconda3/envs/dev/lib/python3.9/site-packages/small_fish_gui/pipeline/actions.py", line 75, in add_detection
+    detection_parameters = initiate_detection(
+  File "/home/floric/miniconda3/envs/dev/lib/python3.9/site-packages/small_fish_gui/pipeline/detection.py", line 227, in initiate_detection
+    detection_parameters['spot_size_z'] = round(detection_parameters['voxel_size_z']*1.5) if isinstance(detection_parameters['voxel_size_z'], (float,int)) else None
+KeyError: 'voxel_size_z'

{small_fish_gui-1.10.3 → small_fish_gui-1.10.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.10.3"
+version = "1.10.4"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]
@@ -35,7 +35,7 @@ dependencies = [
 "openpyxl==3.1.2",
 "pyarrow==11.0.0",
 "aicsimageio>=4.14.0",
-
+"aicspylibczi==3.3.1",
 ]
 
 [project.urls]

{small_fish_gui-1.10.3 → small_fish_gui-1.10.4}/src/small_fish_gui/__init__.py

@@ -37,7 +37,7 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """
-__version__ = "1.10.3"
+__version__ = "1.10.4"
 __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
 
 import os

{small_fish_gui-1.10.3 → small_fish_gui-1.10.4}/src/small_fish_gui/gui/_napari_widgets.py

@@ -56,7 +56,7 @@ class ClusterWizard(ABC) :
 CLUSTER_WIZARDS = []
 def register_cluster_wizard(cls):
     """
-    Helper to register all clusters related class
+    Helper to register all clusters related wizard class. Object to be instanciated upon launching napari but that have no widget.
     """
     CLUSTER_WIZARDS.append(cls)
     return cls
@@ -198,6 +198,8 @@ class ClusterIDSetter(ClusterWidget) :
                     new_spot_number = len(self.single_layer.features.loc[self.single_layer.features['cluster_id'] == cluster_id])
                     self.cluster_layer.features.loc[self.cluster_layer.features['cluster_id'] == cluster_id, ["spot_number"]] = new_spot_number
                 self.cluster_layer.events.features()
+            else :
+                print(f"Not cluster with id {cluster_id} was found.")
 
             self.cluster_layer.selected_data.clear()
 
@@ -490,7 +492,6 @@ class ClusterCleaner(ClusterWizard) :
 
         def delete_empty_cluster() :
             drop_idx = self.cluster_layer.features[self.cluster_layer.features['spot_number'] == 0].index
-            print("drop_idx : ",drop_idx)
             
             if len(drop_idx) > 0 :
                 print("Removing {} empty cluster(s)".format(len(drop_idx)))

{small_fish_gui-1.10.3 → small_fish_gui-1.10.4}/src/small_fish_gui/pipeline/detection.py

@@ -218,9 +218,9 @@ def initiate_detection(user_parameters : pipeline_parameters, map_, shape) :
         pass
     else :
         detection_parameters['voxel_size'] = [round(v) if isinstance(v, (float,int)) else None for v in voxel_size]
-        detection_parameters['voxel_size_z'] = detection_parameters['voxel_size'][0]
-        detection_parameters['voxel_size_y'] = detection_parameters['voxel_size'][1]
-        detection_parameters['voxel_size_x'] = detection_parameters['voxel_size'][2]
+        detection_parameters['voxel_size_z'] = detection_parameters['voxel_size'][0] if isinstance(detection_parameters['voxel_size'][0], (float,int)) else None
+        detection_parameters['voxel_size_y'] = detection_parameters['voxel_size'][1] if isinstance(detection_parameters['voxel_size'][1], (float,int)) else None
+        detection_parameters['voxel_size_x'] = detection_parameters['voxel_size'][2] if isinstance(detection_parameters['voxel_size'][2], (float,int)) else None
 
     #Setting default spot size to 1.5 voxel
     if detection_parameters.get('spot_size') is None :

{small_fish_gui-1.10.3 → small_fish_gui-1.10.4}/src/small_fish_gui/requirements.txt

@@ -15,4 +15,5 @@ scikit-image==0.19.1
 scikit-learn==1.3.2
 openpyxl>=3.1.2
 pyarrow>=11.0.0
-aicsimageio>=aicsimageio==4.14.0
+aicsimageio>=aicsimageio==4.14.0
+aicspylibczi==3.3.1