small-fish-gui 1.9.0__tar.gz → 1.9.1__tar.gz

{small_fish_gui-1.9.0 → small_fish_gui-1.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.9.0
+Version: 1.9.1
 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: Issues, https://github.com/2Echoes/small_fish/issues

{small_fish_gui-1.9.0 → small_fish_gui-1.9.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.9.0"
+version = "1.9.1"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]

{small_fish_gui-1.9.0 → small_fish_gui-1.9.1}/src/small_fish_gui/__init__.py

@@ -38,4 +38,4 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 """
-__version__ = "1.9.0"
+__version__ = "1.9.1"

{small_fish_gui-1.9.0 → small_fish_gui-1.9.1}/src/small_fish_gui/batch/pipeline.py

@@ -120,7 +120,7 @@ def batch_pipeline(
         image, other_image = prepare_image_detection(map_, parameters) 
         nucleus_signal = get_nucleus_signal(image, other_image, parameters)
         try : # Catch error raised if user enter a spot size too small compare to voxel size
-            parameters, frame_result, spots, clusters = launch_detection(
+            parameters, frame_result, spots, clusters, spot_cluster_id = launch_detection(
                 image,
                 other_image,
                 parameters,
@@ -139,7 +139,7 @@ def batch_pipeline(
         if parameters['save detection'] :
             if parameters['do_cluster_computation'] : 
                 if len(clusters) > 0 :
-                    spots_list = [spots, clusters[:,:parameters['dim']]]
+                    spots_list = [spots, clusters[:,:-2]]
                 else : spots_list = [spots]
             else : spots_list = [spots]
             output_spot_tiffvisual(
@@ -166,6 +166,7 @@ def batch_pipeline(
                     user_parameters=parameters,
                     image=image,
                     spots=spots,
+                    cluster_id=spot_cluster_id,
                     nucleus_label= nucleus_label,
                     cell_label= cytoplasm_label,
                 )
@@ -178,6 +179,7 @@ def batch_pipeline(
         nucleus_signal = nucleus_signal,
         spots=spots,
         clusters=clusters,
+        spots_cluster_id=spot_cluster_id,
         nucleus_label = nucleus_label,
         cell_label= cytoplasm_label,
         user_parameters=parameters,