small-fish-gui 1.9.3__py3-none-any.whl → 1.10.0__py3-none-any.whl

small_fish_gui/README.md

@@ -1,7 +1,3 @@
-***INSTALATTION ISSUE : Currently the package cannot be installed due to a package deletion on pypi. I will migrate the code to a free, open source gui package and update the dependecies list***
-  
-  --> Requirements have been updated, pip installation is still not working but it is possible to install through git cloning
-
 # Small Fish
 **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.
 
@@ -27,7 +23,7 @@ If you don't have a python installation yet I would recommend the [miniconda dis
 It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.
 
 ```bash
-conda create -n small_fish python=3.8
+conda create -n small_fish python=3.9
 conda activate small_fish
 ```
 Then download the small_fish package : 
@@ -99,9 +95,11 @@ Note that for training it is recommended to first set up your GPU as training co
 Optional features to include in future versions : 
 
 **Major Dev**
-- time stack (which would include cell tracking)
-- 3D segmentation
+* time stack (which would include cell tracking)
+* 3D segmentation
 
 **Minor features**
-- allows npz files with multiple masks in load segmentation by asking user which one to select
-- fix parquet format or replace to another compressed format
+* allows npz files with multiple masks in load segmentation by asking user which one to select
+* fix parquet format or replace to another compressed format
+* In Napari viewer, or add an extra spot layer to visualsize spots that are in foci or color spots that are in clusters in specific color.
+* Foci merge tool in Napari

small_fish_gui/__init__.py

@@ -36,6 +36,9 @@ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 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__ = "1.9.3"
+__version__ = "1.10.0"
+__wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
+
+import os
+os.environ["QT_QPA_PLATFORM"] = "xcb"

small_fish_gui/__main__.py

@@ -1,29 +1,52 @@
-import sys, subprocess
-import FreeSimpleGUI as sg
-
+import sys, subprocess, re
 from small_fish_gui import __version__
 
+AVAILABLE_ARGUMENTS = {
+    ('-v','--v','--version') : "Prompt the software version.",
+    ('--launch', '-l') : "Launch small fish gui, equivalent to no arguments.",
+    ('-h', '--help', '--h') : "Prompt this help menu."
+}
+
+
 def main():
     import small_fish_gui.pipeline.main
 
-def is_last_version() :
-    latest_version = str(subprocess.run([sys.executable, '-m', 'pip', 'install', '{}==random'.format('small_fish_gui')], capture_output=True, text=True))
-    latest_version = latest_version[latest_version.find('(from versions:')+15:]
-    latest_version = latest_version[:latest_version.find(')')]
-    latest_version = latest_version.replace(' ','').split(',')[-1]
-
-    current_version = __version__
+def _get_version() :
+    return __version__
 
-    return current_version == latest_version
+def is_last_version() :
+    
+    query = subprocess.run([sys.executable, '-m', 'pip', 'index', 'versions', 'small_fish_gui'], capture_output=True, text=True)
+    all_version = query.stdout.split(',')
+    latest_version = all_version[0]
+    regex = r"\d+\.\d+\.\d+"
+    latest = re.findall(regex, latest_version)
+    
+    current_version = _get_version()
+    
+    if len(latest) == 0 : 
+        return current_version
+    else :
+        return current_version == latest[-1]
 
 if __name__ == "__main__":
 
     if not is_last_version() :
         print("A new version of Small Fish is available. To update close small fish and type :\npip install --upgrade small_fish_gui")
 
-    try :
-        sys.exit(main())
-    except Exception as error :
-        sg.popup("Sorry. Something went wrong...\nIf you have some time to spare could you please communicate the error you encountered (next window) on :\nhttps://github.com/2Echoes/small_fish/issues.")
-        sg.popup_error_with_traceback(error)
-        raise error
+    arguments = sys.argv
+
+    if len(arguments) > 1 :
+        if arguments[1] in ['-v','--v','--version'] :
+            print(_get_version())
+            quit()
+        elif arguments[1] in ['--launch', '-l'] :
+            pass
+        elif arguments[1] in ['-h', '--help', '--h'] :
+            for key, help in AVAILABLE_ARGUMENTS.items() :
+                print(f"{key} : {help}")
+            quit()
+        else :
+            print(f"Incorrect argument : {arguments}, to launch small fish don't pass any argument or pick amongst {AVAILABLE_ARGUMENTS.keys()}")
+
+    sys.exit(main())

small_fish_gui/batch/prompt.py

@@ -212,7 +212,7 @@ def batch_promp(
     #Hiding options for non batch mode
     window= window.finalize()
     napari_correction_elmt.update(disabled=True)
-    get_elmt_from_key(tab_dict['Input'], key= 'image path').update(disabled=True)
+    get_elmt_from_key(tab_dict['Input'], key= 'image_path').update(disabled=True)
     for key in seg_keys_to_hide : get_elmt_from_key(tab_dict['Segmentation'], key=key).update(disabled=True)
     for key in detection_keys_to_hide : get_elmt_from_key(tab_dict['Detection'], key=key).update(disabled=True)
     

small_fish_gui/batch/update.py

@@ -51,8 +51,8 @@ def update_detection_tab(
     deconvolution_kernel_z = get_elmt_from_key(tab_elmt, key= 'deconvolution_kernel_z')
     
     #Clustering
-    cluster_size = get_elmt_from_key(tab_elmt, key= 'cluster size')
-    min_number_of_spot = get_elmt_from_key(tab_elmt, key= 'min number of spots')
+    cluster_size = get_elmt_from_key(tab_elmt, key= 'cluster_size')
+    min_number_of_spot = get_elmt_from_key(tab_elmt, key= 'min_number_of_spots')
     
     #segmentation and multichannel
     nucleus_channel_signal = get_elmt_from_key(tab_elmt, key= 'nucleus channel signal')

small_fish_gui/batch/values.txt

@@ -2,7 +2,7 @@ List of keys for batch 'values' dict instance :
 
 Batch_folder 
 0
-image path 
+image_path 
 3D stack 
 multichannel 
 Dense regions deconvolution 

small_fish_gui/gui/__init__.py

@@ -5,7 +5,6 @@ This subpackge contains code related to graphical interface
 from .prompts import _error_popup
 from .prompts import _warning_popup 
 from .prompts import prompt
-from .prompts import prompt_with_help
 from .prompts import input_image_prompt
 from .prompts import hub_prompt
 from .prompts import detection_parameters_promt
@@ -13,8 +12,8 @@ from .prompts import coloc_prompt
 from .prompts import output_image_prompt
 from .prompts import ask_cancel_detection
 from .prompts import ask_cancel_segmentation
-from .prompts import ask_help
 from .prompts import ask_detection_confirmation
+from .prompts import prompt_restore_main_menu
 
 #Helpers to build windows
 from .layout import parameters_layout