small-fish-gui 1.9.3__py3-none-any.whl → 1.9.4__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.
 
@@ -99,9 +95,10 @@ 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.

small_fish_gui/__init__.py

@@ -36,6 +36,5 @@ 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__ = "1.9.4"

small_fish_gui/__main__.py

@@ -1,20 +1,32 @@
-import sys, subprocess
-import FreeSimpleGUI as sg
-
+import sys, subprocess, traceback, os, re
 from small_fish_gui import __version__
 
 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]
+def _get_version() :
+    return __version__
 
-    current_version = __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."
+}
 
-    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__":
 
@@ -22,8 +34,29 @@ if __name__ == "__main__":
         print("A new version of Small Fish is available. To update close small fish and type :\npip install --upgrade small_fish_gui")
 
     try :
+        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())
+
     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
+        with open("error_log.txt",'a') as error_log :
+            error_log.writelines([
+                f"version {_get_version()}",
+                f"error : {error}",
+                f"traceback :\n{traceback.format_exc()}",
+            ])
+
+        print(f"error_log saved at {os.getcwd()}/error_log.txt. Please consider reporting this by opening an issue on github.")

small_fish_gui/gui/__init__.py

@@ -15,6 +15,7 @@ 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 

small_fish_gui/gui/prompts.py

@@ -222,7 +222,6 @@ def detection_parameters_promt(
     else : values['dim'] = 2
     return values
 
-
 def ask_replace_file(filename:str) :
     layout = [
         [sg.Text("{0} already exists, replace ?")],
@@ -341,7 +340,6 @@ def ask_cancel_detection() :
     else :
         return True
 
-
 def ask_confirmation(question_displayed : str) :
     layout =[
         [sg.Text(question_displayed, font= 'bold 10')],
@@ -355,7 +353,6 @@ def ask_confirmation(question_displayed : str) :
     else :
         return True
     
-
 def prompt_save_segmentation() -> 'dict[Literal["folder","filename","ext"]]':
     while True :
         relaunch = False
@@ -406,4 +403,29 @@ def prompt_load_segmentation() -> 'dict[Literal["nucleus","cytoplasm"]]':
         if not relaunch : break
 
 
-    return values
+    return values
+
+def prompt_restore_main_menu() -> bool :
+    """
+    Warn user that software will try to go back to main menu while saving parameters, and propose to save results and quit if stuck.
+
+    Returns True if user want to save and quit else False, to raise error close window.
+    """
+
+
+    layout = [
+        [sg.Text("An error was caught while proceeding.\nSoftware can try to save parameters and return to main menu or save results and quit.")],
+        [sg.Button("Return to main menu", key='menu'), sg.Button("Save and quit", key='save')]
+    ]
+
+    window = sg.Window('small fish', layout=layout, margins=(10,10), auto_size_text=True, resizable=True)
+    event, values = window.read(close=True)
+
+    if event is None :
+        return None
+    elif event == "save" :
+        return True
+    elif event == "menu" :
+        return False
+    else :
+        raise AssertionError("Unforseen answer")

small_fish_gui/pipeline/main.py

@@ -2,9 +2,10 @@
 This script is called when software starts; it is the main loop.
 """
 
+import traceback
 import pandas as pd
 import FreeSimpleGUI as sg
-from ..gui import hub_prompt
+from ..gui import hub_prompt, prompt_restore_main_menu
 from .actions import add_detection, save_results, compute_colocalisation, delete_acquisitions, rename_acquisitions, save_segmentation, load_segmentation, segment_cells
 from ._preprocess import clean_unused_parameters_cache
 from ..batch import batch_promp
@@ -109,5 +110,21 @@ while True : #Break this loop to close small_fish
 
     except Exception as error :
         sg.popup(str(error))
-        raise error
+
+        save_quit = prompt_restore_main_menu()
+
+        if save_quit is None :
+            raise error
+
+        elif save_quit :
+            save_results(
+                result_df=result_df,
+                cell_result_df=cell_result_df,
+                global_coloc_df=global_coloc_df,
+                cell_coloc_df = cell_coloc_df,
+            )
+            quit()
+        else :
+            continue
+
 quit()

{small_fish_gui-1.9.3.dist-info → small_fish_gui-1.9.4.dist-info}/METADATA

@@ -1,8 +1,9 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.9.3
+Version: 1.9.4
 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
 Project-URL: Issues, https://github.com/2Echoes/small_fish/issues
 Author-email: Slimani Floric <floric.slimani@live.com>
 License-File: LICENSE

{small_fish_gui-1.9.3.dist-info → small_fish_gui-1.9.4.dist-info}/RECORD

@@ -1,8 +1,8 @@
 small_fish_gui/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui/README.md,sha256=4Nf5uOLMlNoX-3Kb9KZclLzPUAxWNAMi9el2a_7I9kA,4829
+small_fish_gui/README.md,sha256=rhcqAWtQWPEmheUzChY_ok-ytAkZlboNQHdx19LRutw,4643
 small_fish_gui/Segmentation example.jpg,sha256=opfiSbjmfF6z8kBs08sg_FNR2Om0AcMPU5sSwSLHdoQ,215038
-small_fish_gui/__init__.py,sha256=OM_dE2QL2JVZ_bqEZmk2UdSJCocITwnLP3M5MzBs4as,1941
-small_fish_gui/__main__.py,sha256=Ssw1cF5FxExyEeFcRHEZYX_q7VNUExZkQ3wjQBotRNQ,1145
+small_fish_gui/__init__.py,sha256=WGaTzQTK6LJ7mTFtO3En_DlnGCBHIf8HLnam2jRXKjk,1940
+small_fish_gui/__main__.py,sha256=ngHNZr9ui8FTE9FPUJ9ULFGMs-5Wenpbcq__wAwFOAI,2128
 small_fish_gui/hints.py,sha256=_AhC-Th36ELxinjMyGtjIqJfZkISPr1YwhQ9ifD9Kj4,1926
 small_fish_gui/napari_detection_example.png,sha256=l5EZlrbXemLiGqb5inSVsD6Kko1Opz528-go-fBfrw8,977350
 small_fish_gui/requirements.txt,sha256=z8iaxqarErZuMpmRKqcW07nfb_tQAOOkQ4LQSA9ovCk,322
@@ -17,13 +17,13 @@ small_fish_gui/batch/test.py,sha256=FcoCngSeueociwVoG8V3C6lQO7rrRHUfIVA2hJKr4v4,
 small_fish_gui/batch/update.py,sha256=uVenjjJBHZ3MeW5b20HzlSBueu3QZWEGLIEHRnPm-Tg,5044
 small_fish_gui/batch/utils.py,sha256=Pnmzlen8gmLBYBthMiUiK0TErjBBSId9SjKeBd9U6-U,1784
 small_fish_gui/batch/values.txt,sha256=eS19O1pdj0HYfwGUlWIpkvfNZQFxA3F4BDR8qahXh28,999
-small_fish_gui/gui/__init__.py,sha256=xQ_BfYcnQmKZtx_0leO4OmbkLNLv49ZPqEu_UXMgmDc,867
+small_fish_gui/gui/__init__.py,sha256=-t93Mz9AkpZsTH3XdYGj5-CXJNbWJ62k40QTWgpAGQA,913
 small_fish_gui/gui/_napari_widgets.py,sha256=8IMppaPZU37ANdZwTZOhwqCEly0hokzYL7UIVIixGns,3022
 small_fish_gui/gui/animation.py,sha256=MnYsA1kxQZ72L_H0knxOs41lG0ZZv1re7gSgYNmZY00,983
 small_fish_gui/gui/help_module.py,sha256=_6ZTiCym1uYJTlKekPSmGCXQVr6z7TRaxEhRAL90Eko,9614
 small_fish_gui/gui/layout.py,sha256=ew5d3Mlr0DnC3j3uCWBzykEHJ8faa4wmKHZbiNOjdJY,14188
 small_fish_gui/gui/napari_visualiser.py,sha256=AmpUErfko1ZamYoORRsgR4JT9xRzQKpi-sFok-FFKtg,14569
-small_fish_gui/gui/prompts.py,sha256=1J1pohfNR0FBwqyUUp-fdA4IEH389Ope2KxVq_3bjrY,15408
+small_fish_gui/gui/prompts.py,sha256=Kqqhb3DJujHE3NNWMZKMTBQ7h1B79GicvdnaG4i3HG4,16301
 small_fish_gui/gui/testing.ipynb,sha256=5xoMDR2a3aa4q8KoEoJ22HrcWDyHkCF4arVeVVm7ovs,71500
 small_fish_gui/gui/screenshot/general_help_screenshot.png,sha256=X4E6Td5f04K-pBUPDaBJRAE3D5b8fuEdiAUKhkIDr-0,54210
 small_fish_gui/gui/screenshot/mapping_help_screenshot.png,sha256=HcuRh5TYciUogUasza5vZ_QSshaiHsskQK23mh9vQS8,34735
@@ -39,13 +39,13 @@ small_fish_gui/pipeline/_preprocess.py,sha256=f8TSoieM8PXgEVemnOa1zW8LrfXdE9ZZ61
 small_fish_gui/pipeline/_signaltonoise.py,sha256=7A9t7xu7zghI6cr201Ldm-LjJ5NOuP56VSeJ8KIzcUo,8497
 small_fish_gui/pipeline/actions.py,sha256=YLuRoVwG0bdQ3LvwQDrObQZaHzsOMlntrayfxY13OCw,15941
 small_fish_gui/pipeline/detection.py,sha256=Pe_1e8FKqvVyhuDOPdb2LmDKpuvS7Vg1IXWX83HqTz4,35556
-small_fish_gui/pipeline/main.py,sha256=EmFiQoA86uLOmVAKZFjXW-wbgcQtCFMdFHKnkNUbZ1U,4831
+small_fish_gui/pipeline/main.py,sha256=X8xyTXxNIgK25LO7X29BpIglR5zwEHh8fpyaROLD7HE,5260
 small_fish_gui/pipeline/segmentation.py,sha256=8oZVs6EF0cE89OfauR_sxpzf9uxtqjAuzi5FxkbOS7Q,19913
 small_fish_gui/pipeline/spots.py,sha256=9hNOGnOZhrtrIORt8UGBcI-SGCh1XftcUGerkBwN-QY,2201
 small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
 small_fish_gui/pipeline/testing.ipynb,sha256=Rs7VQ7TImNyUzT2_59JgbOjR5_Qs-0NjHHnqS87eiwA,76481
 small_fish_gui/pipeline/utils.py,sha256=run6qtqCAe_mFnE3o1CnmF1xBBmK3ydgc8-jOV9P-_w,448
-small_fish_gui-1.9.3.dist-info/METADATA,sha256=9_cLPkb_KqtU1no-mlAqrJL9z04IwpFYNkNnmrLnFqE,2568
-small_fish_gui-1.9.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-small_fish_gui-1.9.3.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui-1.9.3.dist-info/RECORD,,
+small_fish_gui-1.9.4.dist-info/METADATA,sha256=Bgc5DOz2cWZrBxt8V9ePZ2d40tTDmDwhDcYp9yHGKgk,2634
+small_fish_gui-1.9.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+small_fish_gui-1.9.4.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
+small_fish_gui-1.9.4.dist-info/RECORD,,