lots of fixes

.gitignore

@@ -3,4 +3,10 @@
 
 logs/*
 
-.pyc
+.pyc
+__pycache__/*
+
+build
+dist
+
+*.build

anon_gui.cmd

@@ -0,0 +1,6 @@
+
+@echo off
+rem This script was created by Nuitka to execute 'anon_gui.exe' with Python DLL being found.
+set PATH=C:\PROGRA~1\PYTHON~1;%PATH%
+set PYTHONHOME=C:\Program Files\Python311
+"%~dp0anon_gui.exe" %*

anon_gui.py

@@ -55,8 +55,11 @@ import hashlib
 
 try:
     from agw import hyperlink as hl
+    from agw import pygauge as PG
 except ImportError:  # if it's not there locally, try the wxPython lib.
     import wx.lib.agw.hyperlink as hl
+    import wx.lib.agw.pygauge as PG
+
 
 
 import wx.lib.agw.thumbnailctrl as TC
@@ -565,7 +568,7 @@ class AnonGui(wx.App):
         self.series_grid = SeriesGrid(self.panel)
 
         if self.clear_files_on_start:
-            self.ClearFiles()
+            self.ClearFiles(load_dir=False)
 
         self.panel.sizer = wx.BoxSizer(wx.VERTICAL)
 
@@ -627,7 +630,6 @@ class AnonGui(wx.App):
         self.list_ctrl.InsertColumn(6, "Hash")
         self.list_ctrl.InsertColumn(7, "Series Instance UID")
 
-        self.AnnonymiseFilesInDir(self.input_dir, self.dir)
 
         # self.UpdateListCtrl()
 
@@ -673,12 +675,23 @@ class AnonGui(wx.App):
         self.panel.sizer.Add(self.drag_button, 2, wx.EXPAND)
         self.panel.sizer.Add(self.upload_button, 2, wx.EXPAND)
 
+        self.progress_sizer = wx.BoxSizer(wx.VERTICAL)
+        self.progress_bar = wx.Gauge(self.panel, style=wx.GA_HORIZONTAL|wx.GA_PROGRESS)
+        #self.progress_bar = PG.PyGauge(self.panel, style=wx.GA_HORIZONTAL|wx.GA_PROGRESS)
+        #self.progress_bar.SetDrawValue(draw=True, drawPercent=True, font=None, colour=wx.RED, formatString=None)
+        self.progress_text = wx.StaticText(self.panel, label="Text")
+        self.progress_sizer.Add(self.progress_bar, 2, wx.EXPAND)
+        self.progress_sizer.Add(self.progress_text, 2, wx.EXPAND)
+        self.panel.sizer.Add(self.progress_sizer, 2, wx.EXPAND)
+        self.progress_sizer.ShowItems(show=False)
+
         # Layout sizers
         self.panel.SetSizer(self.panel.sizer)
         self.panel.SetAutoLayout(1)
         self.panel.sizer.Fit(self.panel)
         self.frame.Show()
         # self.spinner.Hide()
+        self.AnnonymiseFilesInDir(self.input_dir, self.dir)
 
         self.Bind(wx.EVT_KEY_DOWN, self.onKeyPress)
 
@@ -717,29 +730,57 @@ class AnonGui(wx.App):
 
         #files = order_files_by_dicom_attribute(files)
 
-        progress_dialog = wx.ProgressDialog(
+        #progress_dialog = wx.ProgressDialog(
-            "Annonymise files",
+        #    "Annonymise files",
-            "Removing data...",
+        #    "Removing data...",
-            maximum=len(files),
+        #    maximum=len(files),
-            style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME,
+        #    style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME,
-        )
+        #)
+        with self.progress(len(files), "Annonymise files") as p:
+            #p.SetRange(len(files))
 
-        for n, file in enumerate(files):
+            for n, file in enumerate(files):
-            progress_dialog.Update(n)
+                #progress_dialog.Update(n)
-            new_filepath: Path
+                p.update(n)
-            # Get next available filename
+                new_filepath: Path
-            i: int = 0
+                # Get next available filename
-            while os.path.exists(
+                i: int = 0
-                new_filepath := output_dir.joinpath(f"IMG_{i:03}.dcm")
+                while os.path.exists(
-            ):
+                    new_filepath := output_dir.joinpath(f"IMG_{i:03}.dcm")
-                i += 1
+                ):
-                # new_filepath = Path(output_dir).joinpath(f"IMG_{i:03}.dcm")
+                    i += 1
+                    # new_filepath = Path(output_dir).joinpath(f"IMG_{i:03}.dcm")
 
-            dataset, filepath = anonymize_file(file, new_filepath)
+                dataset, filepath = anonymize_file(file, new_filepath)
-            self.add_datails_to_file_detail_map(dataset, filepath)
+                self.add_datails_to_file_detail_map(dataset, filepath)
-        progress_dialog.Destroy()
+        #progress_dialog.Destroy()
 
         self.LoadDir(self.dir)
+    
+    @contextlib.contextmanager
+    def progress(self, total: int, text: str="Working"):
+        #self.progress_sizer.Show()
+        self.progress_text.SetLabelText(text)
+        self.progress_bar.SetRange(total)
+        self.progress_sizer.ShowItems(show=True)
+        self.panel.Layout()
+        #self.panel.sizer.Fit(self.panel)
+        try:
+            class P():
+                def __init__(self, gui, total, text):
+                    self.gui  = gui
+                    self.text = text
+                    self.total = total
+                def update(self, n: int):
+                    self.gui.progress_bar.SetValue(n)
+                    self.gui.progress_text.SetLabelText(f"{self.text} : {n}")
+            yield P(self, total, text)
+        finally:
+            #self.progress_sizer.Hide()
+            self.progress_sizer.ShowItems(show=False)
+            self.panel.Layout()
+            #self.panel.SetAutoLayout(1)
+            #self.panel.sizer.Fit(self.panel)
 
     def onKeyPress(self, event):
         keycode = event.GetKeyCode()
@@ -774,7 +815,7 @@ class AnonGui(wx.App):
 
     def OnExit(self):
         if self.clear_files_on_close:
-            self.ClearFiles()
+            self.ClearFiles(load_dir=False)
 
         # self.zmq_thread.join()
 
@@ -915,11 +956,13 @@ class AnonGui(wx.App):
 
         dlg.ShowModal()
 
-    def ClearFiles(self, event=None):
+    def ClearFiles(self, event=None, load_dir: bool=True):
         files = Path(self.dir).glob("*")
         for f in files:
             os.remove(f)
-        self.LoadDir(clear_file_detail_map=True)
+        
+        if load_dir:
+            self.LoadDir(clear_file_detail_map=True)
 
     def add_datails_to_file_detail_map(self, dataset, file):
         try:
@@ -1018,66 +1061,69 @@ class AnonGui(wx.App):
         n = 0
         DATA = {}
 
-        progress_dialog = wx.ProgressDialog(
+        #progress_dialog = wx.ProgressDialog(
-            "Loading files",
+        #    "Loading files",
-            "Extracting data from files",
+        #    "Extracting data from files",
-            maximum=len(self.files),
+        #    maximum=len(self.files),
-            style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME,
+        #    style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME,
-        )
+        #)
+        with self.progress((len(self.files)), "Loading files") as p:
+            #p.SetRange(len(self.files))
 
-        self.series_map = defaultdict(list)
+            self.series_map = defaultdict(list)
-        self.series_map_details = defaultdict(dict)
+            self.series_map_details = defaultdict(dict)
 
-        hashes = []
+            hashes = []
 
-        for n, f in enumerate(self.files):
+            for n, f in enumerate(self.files):
-            progress_dialog.Update(n)
+                #progress_dialog.Update(n)
-            # dataset = pydicom.read_file(f)
+                p.update(n)
+                # dataset = pydicom.read_file(f)
 
-            if f in self.file_detail_map:
+                if f in self.file_detail_map:
-                d, hash, d2 = self.file_detail_map[f]
+                    d, hash, d2 = self.file_detail_map[f]
-                print("in map")
+                    print("in map")
-            else:
+                else:
+                    try:
+                        dataset = pydicom.dcmread(f)
+                    except FileNotFoundError:
+                        return
+
+                    print("recalc")
+                    d, hash, d2 = self.add_datails_to_file_detail_map(dataset, f)
+
+                hashes.append(hash)
+
+
+                series_instances_uid = d2["series_instances_uid"]
                 try:
-                    dataset = pydicom.dcmread(f)
+                    self.series_map[series_instances_uid].append(f)
-                except FileNotFoundError:
+                    self.series_map_details[series_instances_uid][
-                    return
+                        "series_description"
+                    ] = d2["series_description"]
+                    self.series_map_details[series_instances_uid]["study_description"] = d2[
+                        "study_description"
+                    ]
+                    self.series_map_details[series_instances_uid]["name"] = d2["name"]
+                except:
+                    logger.debug(f"Unable to get Series Instance UID: {f.name}")
 
-                print("recalc")
+                logger.debug(d)
-                d, hash, d2 = self.add_datails_to_file_detail_map(dataset, f)
+                DATA[n] = d
+                self.list_ctrl.Append(d)
+                self.list_ctrl.SetItemPyData(n, {"file": f, "hash": hash})
+                self.list_ctrl.SetItemData(n, n)
 
-            hashes.append(hash)
+                if f in self.file_duplicate_check:
+                    if self.file_duplicate_check[f]["id"]:
+                        self.list_ctrl.SetItemBackgroundColour(n, wx.RED)
 
-
+                n = n + 1
-            series_instances_uid = d2["series_instances_uid"]
-            try:
-                self.series_map[series_instances_uid].append(f)
-                self.series_map_details[series_instances_uid][
-                    "series_description"
-                ] = d2["series_description"]
-                self.series_map_details[series_instances_uid]["study_description"] = d2[
-                    "study_description"
-                ]
-                self.series_map_details[series_instances_uid]["name"] = d2["name"]
-            except:
-                logger.debug(f"Unable to get Series Instance UID: {f.name}")
-
-            logger.debug(d)
-            DATA[n] = d
-            self.list_ctrl.Append(d)
-            self.list_ctrl.SetItemPyData(n, {"file": f, "hash": hash})
-            self.list_ctrl.SetItemData(n, n)
-
-            if f in self.file_duplicate_check:
-                if self.file_duplicate_check[f]["id"]:
-                    self.list_ctrl.SetItemBackgroundColour(n, wx.RED)
-
-            n = n + 1
         self.list_ctrl.UpdateData(DATA)
         self.populate_series_grid()
 
 
-        progress_dialog.Destroy()
+        #progress_dialog.Destroy()
 
         #if hashes:
         #    self.check_image_hashes(hashes)
@@ -1110,8 +1156,8 @@ class AnonGui(wx.App):
                 for hash, dup in resp.json().items():
                     self.file_duplicate_check[hash_file_map[hash]] = dup
 
-                print(self.file_duplicate_check)
+                if resp.json().items():
-                wx.CallAfter(self.UpdateListCtrl)
+                    wx.CallAfter(self.UpdateListCtrl)
             self.image_hash_check_in_progress = False
 
     def OnColRightClick(self, event):
@@ -1134,52 +1180,55 @@ class AnonGui(wx.App):
             files_to_upload[i : i + n] for i in range(0, len(files_to_upload), n)
         ]
 
-        progress_dialog = wx.ProgressDialog(
+        #progress_dialog = wx.ProgressDialog(
-            "Uploading files",
+        #    "Uploading files",
-            "Uploading files. This is done in batches...",
+        #    "Uploading files. This is done in batches...",
-            maximum=len(chunked_files),
+        #    maximum=len(chunked_files),
-            style=wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME,
+        #    style=wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME,
-        )
+        #)
+        with self.progress(len(chunked_files), "Uploading files (in batches)") as p:
+            #p.SetRange(len(chunked_files))
 
-        upload_file_list = []
+            upload_file_list = []
-        duplicate_file_list = []
+            duplicate_file_list = []
 
-        for n, files in enumerate(chunked_files):
+            for n, files in enumerate(chunked_files):
 
-            def upload_files(files):
+                def upload_files(files):
-                self.rqst.headers["X-CSRFToken"] = self.rqst.cookies["csrftoken"]
+                    self.rqst.headers["X-CSRFToken"] = self.rqst.cookies["csrftoken"]
-                # print(self.rqst.headers)
+                    # print(self.rqst.headers)
-                # print(self.rqst.cookies)
+                    # print(self.rqst.cookies)
-                resp = self.rqst.post(
+                    resp = self.rqst.post(
-                    f"{self.base_site_url}/api/atlas/upload_dicom",
+                        f"{self.base_site_url}/api/atlas/upload_dicom",
-                    # data=data,
+                        # data=data,
-                    files=files,
+                        files=files,
-                )
+                    )
 
-                logger.debug(f"Resp: {resp}")
+                    logger.debug(f"Resp: {resp}")
-                logger.debug(f"{resp.content}")
+                    logger.debug(f"{resp.content}")
-                return resp
+                    return resp
 
-            progress_dialog.Update(n, f"Uploading batch {n}/{len(chunked_files)}")
+                p.update(n)
+                #progress_dialog.Update(n, f"Uploading batch {n}/{len(chunked_files)}")
 
-            logger.debug(f"n: {n}")
+                logger.debug(f"n: {n}")
-            # try to upload the files
+                # try to upload the files
-            resp = upload_files(files)
+                resp = upload_files(files)
-            if resp.status_code == 200:
+                if resp.status_code == 200:
-                upload_file_list.extend(resp.json()["uploaded"])
+                    upload_file_list.extend(resp.json()["uploaded"])
-                duplicate_file_list.extend(resp.json()["duplicates"])
+                    duplicate_file_list.extend(resp.json()["duplicates"])
 
-                continue
+                    continue
 
-            logger.debug(f"n: {n} fail")
+                logger.debug(f"n: {n} fail")
-            # try again if we fail
+                # try again if we fail
-            resp = upload_files(files)
+                resp = upload_files(files)
-            if resp.status_code == 200:
+                if resp.status_code == 200:
-                upload_file_list.extend(resp.json()["uploaded"])
+                    upload_file_list.extend(resp.json()["uploaded"])
-                duplicate_file_list.extend(resp.json()["duplicates"])
+                    duplicate_file_list.extend(resp.json()["duplicates"])
-                continue
+                    continue
 
-        progress_dialog.Destroy()
+        #progress_dialog.Destroy()
 
         print(upload_file_list)
         print(duplicate_file_list)
@@ -1213,10 +1262,10 @@ class AnonGui(wx.App):
 @app.callback(invoke_without_command=True)
 def runGUI(
     ctx: typer.Context,
-    #input_dir: Path = "C:\\Temp\\",
+    input_dir: Path = "C:\\Temp\\",
-     input_dir: Path = "/home/ross/temp/in/",
+    #input_dir: Path = "/home/ross/temp/in/",
-    #output_dir: Path = "C:\\temp_upload\\",
+    output_dir: Path = "C:\\temp_upload\\",
-     output_dir: Path = "/home/ross/temp/out/",
+    #output_dir: Path = "/home/ross/temp/out/",
     silent_fail: bool = False,
     clear_files: bool = True,
     clear_files_on_close: bool = True,

anon_gui.spec

@@ -1,33 +1,24 @@
 # -*- mode: python ; coding: utf-8 -*-
 
 
-block_cipher = None
-
-
 a = Analysis(
     ['anon_gui.py'],
     pathex=[],
-    #binaries=[(r"C:\Users\krugerro\Desktop\rad_tools\.venv\Lib\site-packages\pywin32_system32\pythoncom311.dll", "."), 
+    binaries=[],
-    #(r"C:\Users\krugerro\Desktop\rad_tools\.venv\Lib\site-packages\pywin32_system32\pywintypes311.dll", "."), 
-    #],
     datas=[],
     hiddenimports=[],
     hookspath=[],
     hooksconfig={},
     runtime_hooks=[],
     excludes=[],
-    win_no_prefer_redirects=False,
-    win_private_assemblies=False,
-    cipher=block_cipher,
     noarchive=False,
 )
-pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher)
+pyz = PYZ(a.pure)
 
 exe = EXE(
     pyz,
     a.scripts,
     a.binaries,
-    a.zipfiles,
     a.datas,
     [],
     name='anon_gui',
@@ -37,7 +28,7 @@ exe = EXE(
     upx=True,
     upx_exclude=[],
     runtime_tmpdir=None,
-    console=True,
+    console=False,
     disable_windowed_traceback=False,
     argv_emulation=False,
     target_arch=None,

requirements.txt

@@ -0,0 +1,12 @@
+typer
+wxpython
+pydicom
+dicognito
+python-datauri
+bs4
+requests
+zmq
+blake3
+loguru
+dicom2jpg
+pyinstaller