small-fish-gui 1.9.1__tar.gz → 1.9.2__tar.gz

{small_fish_gui-1.9.1 → small_fish_gui-1.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.9.1
+Version: 1.9.2
 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-1.9.1 → small_fish_gui-1.9.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.9.1"
+version = "1.9.2"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]

{small_fish_gui-1.9.1 → small_fish_gui-1.9.2}/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__ = "1.9.1"
+__version__ = "1.9.2"

{small_fish_gui-1.9.1 → small_fish_gui-1.9.2}/src/small_fish_gui/gui/napari_visualiser.py

@@ -123,7 +123,7 @@ def __update_clusters(new_clusters: np.ndarray, spots: np.ndarray, voxel_size, c
     Outdated. previous behaviour.
     """
     if len(new_clusters) == 0 : return new_clusters
-    if len(spots) == 0 : return np.empty(shape=(0,2+len(voxel_size)))
+    if len(spots) == 0 : return np.empty(shape=(0,2+len(voxel_size)), dtype=int)
 
     if len(new_clusters[0]) in [2,3] :
         new_clusters = np.concatenate([
@@ -198,7 +198,7 @@ def correct_spots(
         if len(clusters) > 0 :
             clusters_coordinates = clusters[:, :dim]
         else :
-            clusters_coordinates = np.empty(shape=(0,3)) 
+            clusters_coordinates = np.empty(shape=(0,3), dtype=int) 
         Viewer.add_points( # cluster; this layer can be update by user.
             clusters_coordinates, 
             size = 10, 
@@ -222,14 +222,13 @@ def correct_spots(
     if type(clusters) != type(None) :
         new_clusters = np.round(Viewer.layers['foci'].data).astype(int)
         if len(new_clusters) == 0 :
-            new_clusters = np.empty(shape=(0,5))
+            new_clusters = np.empty(shape=(0,5), dtype=int)
             new_cluster_id = -1 * np.ones(len(new_spots))
             new_spots = np.concatenate([new_spots, new_cluster_id], axis=1)
         else :
             new_cluster_id = Viewer.layers['foci'].features.to_numpy()
             new_clusters = np.concatenate([new_clusters, new_cluster_id], axis=1)
 
-            print("After concatenate new clusters shape = {0}".format(new_clusters.shape))
     
             new_spots, new_clusters = _update_clusters(
                 old_spots =spots,
@@ -243,7 +242,6 @@ def correct_spots(
                 null_value= -2
             )
     
-            print("After _update_cluster\nnew_clusters shape = {0}\nnew_spots shape = {1}".format(new_clusters.shape, new_spots.shape))
 
     else : new_clusters = None
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.2}/src/small_fish_gui/pipeline/detection.py

@@ -183,7 +183,7 @@ def cluster_detection(spots, voxel_size, radius = 350, nb_min_spots = 4, keys_to
     elif isinstance(keys_to_compute, list) : pass
     else : raise TypeError("Wrong type for keys_to_compute. Should be list[str] or str. It is {0}".format(type(keys_to_compute)))
     if len(spots) == 0 :
-        res = {'clustered_spots' : [], 'clusters' : [], 'clustered_spots_dataframe' : pd.DataFrame(columns= ["id", "cluster_id", "z", "y", "x"]), 'clusters_dataframe' : pd.DataFrame(columns= ["id", "z", "y", "x", "spot_number"])}
+        res = {'clustered_spots' : np.empty(shape=(0,len(voxel_size) + 1), dtype=int), 'clusters' : np.empty(shape=(0,len(voxel_size) + 2), dtype=int), 'clustered_spots_dataframe' : pd.DataFrame(columns= ["id", "cluster_id", "z", "y", "x"]), 'clusters_dataframe' : pd.DataFrame(columns= ["id", "z", "y", "x", "spot_number"])}
         return {key : res[key] for key in keys_to_compute}
     else : res = {}
     voxel_size = tuple([int(d) for d in voxel_size])
@@ -192,7 +192,7 @@ def cluster_detection(spots, voxel_size, radius = 350, nb_min_spots = 4, keys_to
 
     if 'clustered_spots' in keys_to_compute :
         res['clustered_spots'] = clustered_spots
-        
+        voxel_size
     if 'clusters' in keys_to_compute : 
         res['clusters'] = clusters
 
@@ -407,9 +407,8 @@ def launch_cell_extraction(
 
     if do_clustering :
         if len(clusters) > 0 :
-
-            free_spots = spots[spots_cluster_id == -1]
-            clustered_spots = spots[spots_cluster_id != -1]
+            free_spots = spots[spots_cluster_id == -1].astype(int)
+            clustered_spots = spots[spots_cluster_id != -1].astype(int)
 
             other_coords = {
                 'clusters_coords' : clusters,
@@ -471,6 +470,13 @@ def launch_cell_extraction(
         free_spots_coords = cell.get('free_spots')
         signal = cell['image']
 
+        if do_clustering :
+            if len(clusters) > 0 :
+                compute_foci = True
+            else : 
+                compute_foci = False
+        else : compute_foci = False
+
         with np.errstate(divide= 'ignore', invalid= 'ignore') :
             features = classification.compute_features(
                 cell_mask=cell_mask,
@@ -485,7 +491,7 @@ def launch_cell_extraction(
                 compute_area=True,
                 compute_dispersion=True,
                 compute_distance=True,
-                compute_foci= do_clustering and len(clusters) > 0,
+                compute_foci= compute_foci,
                 compute_intranuclear=True,
                 compute_protrusion=False,
                 compute_topography=True
@@ -535,7 +541,8 @@ def launch_cell_extraction(
 
         features = [acquisition_id, cell_id, cell_bbox] + features
         features += [rna_coords, foci_coords, clustered_spots_coords, free_spots_coords]
-        features += [len(clustered_spots_coords), len(free_spots_coords)]
+        features += [len(clustered_spots_coords) if type(clustered_spots_coords) != type(None) else None]
+        features += [len(free_spots_coords) if type(free_spots_coords) != type(None) else None]
         
         result_frame = pd.concat([
             result_frame,