small-fish-gui 2.1.1__py3-none-any.whl → 2.1.2__py3-none-any.whl

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__ = "2.1.1"
+__version__ = "2.1.2"
 __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
 
 import os, platform

small_fish_gui/gui/layout.py

@@ -119,6 +119,8 @@ def path_layout(keys= [],look_for_dir = False, header=None, preset=settings.work
     check_parameter(keys= list, header = (str, type(None)))
     for key in keys : check_parameter(key = str)
     
+    initial_folder = preset if preset != "" else settings.working_directory
+
     if look_for_dir : Browse = sg.FolderBrowse
     else : Browse = sg.FileBrowse
 
@@ -446,7 +448,7 @@ def _detection_layout(
         keys=['spots_extraction_folder'],
         look_for_dir=True,
         header= "Individual spot extraction",
-        preset= default_dict.setdefault('spots_extraction_folder', default.spot_extraction_folder)
+        preset= default_dict.setdefault('spots_extraction_folder', "")
     )
     default_filename = default_dict.setdefault("filename","") + "_spot_extraction"
     layout += parameters_layout(

small_fish_gui/gui/napari_visualiser.py

@@ -46,7 +46,7 @@ def correct_spots(
                 axis=0
             )
     if dim == 3 and type(nucleus_label) != type(None) :
-        if nucleus_label == 2 :
+        if nucleus_label.ndim == 2 :
             nucleus_label = np.repeat(
                 nucleus_label[np.newaxis],
                 repeats= len(image),
@@ -171,7 +171,7 @@ def correct_spots(
         if cell_label.ndim == 2 :
             new_cell_label = new_cell_label.max(axis=0)
     if dim == 3 and type(nucleus_label) != type(None) :
-        if nucleus_label == 2 :
+        if nucleus_label.ndim == 2 :
             new_nucleus_label = new_nucleus_label.max(axis=0)
             
 

small_fish_gui/interface/settings.json

@@ -1,5 +1,5 @@
 {
-    "working_directory": "/home/floric/Documents/fish_images",
+    "working_directory": "/media/SSD_floricslimani",
     "do_background_removal": false,
     "background_channel": 0,
     "multichannel_stack": true,
@@ -32,7 +32,7 @@
     "do_dense_regions_deconvolution": false,
     "do_cluster": false,
     "show_napari_corrector": true,
-    "interactive_threshold_selector": true,
+    "interactive_threshold_selector": false,
     "alpha": 0.5,
     "beta": 1.0,
     "gamma": 3.0,
@@ -41,7 +41,7 @@
     "coloc_range": 400,
     "do_csv": false,
     "do_excel": false,
-    "spot_extraction_folder": "/home/floric/my_projects/small_fish_gui",
+    "spot_extraction_folder": "/home/floric",
     "voxel_size": [
         1,
         2,