few updates

.gitignore

@@ -1,4 +1,6 @@
 .env/*
 .venv/*
 
+logs/*
+
 .pyc

anon_gui.py

@@ -1,9 +1,12 @@
 from collections import defaultdict
+import json
 import os
 import threading
 from typing import Iterable
 from bs4 import BeautifulSoup
+import numpy as np
 import requests
+import webbrowser
 
 # from blake3 import blake3
 
@@ -91,7 +94,7 @@ try:
 except TypeError:
     pass
 try:
-    logger.add(os.path.join(application_path, "anon_gui_{time}.log"))
+    logger.add(os.path.join(application_path, "logs", "anon_gui_{time}.log"))
 except TypeError:
     pass
 
@@ -144,7 +147,11 @@ app = typer.Typer(add_completion=False)
 @app.command()
 @logger.catch()
 def annonymise(
-    path: Path, output_dir: Path, run_gui: bool = True, file_list: bool = False
+    path: Path,
+    output_dir: Path,
+    run_gui: bool = True,
+    file_list: bool = False,
+    dev: bool = False,
 ):
     logger.debug(locals())
     if run_gui:  # Let the GUI handle it all
@@ -162,7 +169,7 @@ def annonymise(
     elif path.is_file():
         if file_list:
             with open(path) as f:
-                files = f.read().splitlines()
+                files = [Path(p) for p in f.read().splitlines()]
                 # files = [path]
         else:
             files = [path]
@@ -182,6 +189,7 @@ def annonymise(
 
         anonymize_file(file, new_filepath)
 
+
     # progress_dialog.Destroy()
 
     return new_filepath
@@ -199,7 +207,7 @@ def anonymize_file(file: Path, new_filepath: Path):
     with pydicom.dcmread(file) as dataset:
         anonymizer.anonymize(dataset)
         dataset.save_as(new_filepath)
-        return new_filepath
+        return dataset, new_filepath
 
 
 def order_files_by_dicom_attribute(
@@ -307,7 +315,7 @@ class LoginDialog(wx.Dialog):
         """
         Check credentials and login
         """
-        LOGIN_URL = f"{self.parent.base_site_url}accounts/login/"
+        LOGIN_URL = f"{self.parent.base_site_url}/accounts/login/"
 
         user = self.user.GetValue()
         password = self.password.GetValue()
@@ -355,7 +363,7 @@ class LoginDialog(wx.Dialog):
 
         print(rqst.headers)
         print(rqst.cookies)
-        new = rqst.get(f"{self.parent.base_site_url}accounts/api/atlas/get_cases_user")
+        new = rqst.get(f"{self.parent.base_site_url}/accounts/api/atlas/get_cases_user")
 
         print("CASESE", new)
         print(new.content)
@@ -473,10 +481,10 @@ class AnonGui(wx.App):
         logger.debug(f"Input dir: {input_dir}")
         logger.debug(f"Output dir: {output_dir}")
 
-        self.base_site_url = "https://www.penracourses.org.uk/"
+        self.base_site_url = "https://www.penracourses.org.uk"
 
         if dev:
-            self.base_site_url = "http://localhost:8000/"
+            self.base_site_url = "http://localhost:8000"
 
         self.login_success = False
 
@@ -548,6 +556,7 @@ class AnonGui(wx.App):
         self.panel = wx.Panel(self.frame, wx.ID_ANY)
 
         self.file_detail_map = {}
+        self.file_duplicate_check = {}
 
         self.list_ctrl = SortableList(
             self.panel,
@@ -564,7 +573,7 @@ class AnonGui(wx.App):
             self.panel,
             wx.ID_ANY,
             "Rapid Uploader",
-            URL=f"{self.base_site_url}rapids/create/",
+            URL=f"{self.base_site_url}/rapids/create/",
         )
         # self.panel.sizer.Add(self.link_rapid_upload, 0, wx.ALL, 10)
 
@@ -572,7 +581,7 @@ class AnonGui(wx.App):
             self.panel,
             wx.ID_ANY,
             "Long Series",
-            URL=f"{self.base_site_url}longs/create/series",
+            URL=f"{self.base_site_url}/longs/create/series",
         )
         # self.panel.sizer.Add(self.link_long_upload, 0, wx.ALL, 10)
         hoz_links = wx.BoxSizer(wx.HORIZONTAL)
@@ -615,6 +624,8 @@ class AnonGui(wx.App):
         self.list_ctrl.InsertColumn(3, "Name")
         self.list_ctrl.InsertColumn(4, "Series Description")
         self.list_ctrl.InsertColumn(5, "Slice location")
+        self.list_ctrl.InsertColumn(6, "Hash")
+        self.list_ctrl.InsertColumn(7, "Series Instance UID")
 
         self.AnnonymiseFilesInDir(self.input_dir, self.dir)
 
@@ -662,7 +673,6 @@ class AnonGui(wx.App):
         self.panel.sizer.Add(self.drag_button, 2, wx.EXPAND)
         self.panel.sizer.Add(self.upload_button, 2, wx.EXPAND)
 
-
         # Layout sizers
         self.panel.SetSizer(self.panel.sizer)
         self.panel.SetAutoLayout(1)
@@ -672,6 +682,12 @@ class AnonGui(wx.App):
 
         self.Bind(wx.EVT_KEY_DOWN, self.onKeyPress)
 
+
+        self.image_hash_check_in_progress = False
+        self.duplicate_check_timer = wx.Timer()
+        self.Bind(wx.EVT_TIMER, self.check_image_hashes, self.duplicate_check_timer)
+        self.duplicate_check_timer.Start(2000)
+
         return super().OnInit()
 
     def populate_series_grid(self):
@@ -699,7 +715,7 @@ class AnonGui(wx.App):
 
         logger.debug(files)
 
-        files = order_files_by_dicom_attribute(files)
+        #files = order_files_by_dicom_attribute(files)
 
         progress_dialog = wx.ProgressDialog(
             "Annonymise files",
@@ -719,7 +735,8 @@ class AnonGui(wx.App):
                 i += 1
                 # new_filepath = Path(output_dir).joinpath(f"IMG_{i:03}.dcm")
 
-            anonymize_file(file, new_filepath)
+            dataset, filepath = anonymize_file(file, new_filepath)
+            self.add_datails_to_file_detail_map(dataset, filepath)
         progress_dialog.Destroy()
 
         self.LoadDir(self.dir)
@@ -766,6 +783,7 @@ class AnonGui(wx.App):
     def LoadDir(self, dir=None, refresh=True, clear_file_detail_map=False):
         if clear_file_detail_map:
             self.file_detail_map = {}
+            self.file_duplicate_check = {}
         if dir is None:
             dir = self.dir
         if refresh:
@@ -808,13 +826,23 @@ class AnonGui(wx.App):
         menu.Bind(wx.EVT_MENU, self.DeleteItems, id=1)
         menu.Append(2, "View Dicom")
         menu.Bind(wx.EVT_MENU, self.ViewDicom, id=2)
+
+        for i in range(self.list_ctrl.GetItemCount()):
+            if self.list_ctrl.IsSelected(i):
+                path = self.list_ctrl.GetItemPyData(i)["file"]
+                if path in self.file_duplicate_check and self.file_duplicate_check[path]["id"]:
+                    menu.Append(3, "View on site")
+                    menu.Bind(wx.EVT_MENU, lambda evt: webbrowser.open(f"{self.base_site_url}{self.file_duplicate_check[path]['url']}"), id=3)
+                break
+
+
         self.frame.PopupMenu(menu)
 
     def ViewDicom(self, event):
         selectedItems = []
         for i in range(self.list_ctrl.GetItemCount()):
             if self.list_ctrl.IsSelected(i):
-                #path = self.list_ctrl.GetItemPyData(i["file"])
+                # path = self.list_ctrl.GetItemPyData(i["file"])
                 path = self.list_ctrl.GetItemPyData(i)["file"]
                 print(path)
 
@@ -832,7 +860,7 @@ class AnonGui(wx.App):
         tempdir = Path(tempfile.gettempdir())
         to_move = []
         for i in range(self.list_ctrl.GetItemCount()):
-            path = self.list_ctrl.GetItemPyData(i["file"])
+            path = self.list_ctrl.GetItemPyData(i)["file"]
             logger.debug("--", path)
             # paths.append(path)
             new_path = annonymise(path, tempdir, run_gui=False)
@@ -853,7 +881,7 @@ class AnonGui(wx.App):
         tempdir = Path(tempfile.gettempdir())
         to_move = []
         for i in range(self.list_ctrl.GetItemCount()):
-            path = self.list_ctrl.GetItemPyData(i["file"])
+            path = self.list_ctrl.GetItemPyData(i)["file"]
             logger.debug("--", path)
             # paths.append(path)
 
@@ -873,7 +901,7 @@ class AnonGui(wx.App):
         selectedItems = []
         for i in range(self.list_ctrl.GetItemCount()):
             if self.list_ctrl.IsSelected(i):
-                selectedItems.append(self.list_ctrl.GetItemPyData(i["file"]))
+                selectedItems.append(self.list_ctrl.GetItemPyData(i)["file"])
 
         logger.debug(selectedItems)
         for f in selectedItems:
@@ -893,6 +921,97 @@ class AnonGui(wx.App):
             os.remove(f)
         self.LoadDir(clear_file_detail_map=True)
 
+    def add_datails_to_file_detail_map(self, dataset, file):
+        try:
+            study_desc = dataset.StudyDescription
+        except:
+            study_desc = "..."
+        try:
+            series_desc = dataset.SeriesDescription
+        except:
+            series_desc = "..."
+        try:
+            instance_number = f"{dataset.InstanceNumber:03}"
+        except:
+            instance_number = "..."
+        try:
+            patient_name = str(dataset.PatientName)
+        except:
+            patient_name = "..."
+        try:
+            slice_location = str(dataset.SliceLocation)
+        except:
+            slice_location = "..."
+ 
+
+        series_instances_uid = str(dataset.SeriesInstanceUID)
+        d2 = {
+            "series_instances_uid": series_instances_uid,
+            "series_description": series_desc,
+            "study_description": study_desc,
+            "name": patient_name,
+        }
+
+        #md5 = hashlib.md5()
+        #first = True
+        #for i in dataset.pixel_array.astype(str).flatten():
+        #    if first:
+        #        first = False
+        #        md5.update(f"{i}".encode())
+        #    else:
+        #        md5.update(f",{i}".encode())
+        #md5.update(dataset.PixelData)
+        #md5.update("".join(dataset.pixel_array.astype(str).flatten()).encode())
+        #md5.update(np.char.join("", dataset.pixel_array.astype(str).flatten()).encode())
+        #hash = md5.hexdigest()
+        #print(hash)
+
+        #md5 = hashlib.md5()
+        ##hash = md5.hexdigest()
+        ##md5 = hashlib.md5()
+        ##first = True
+        ##s = ",".join([f"{i}" for i in dataset.pixel_array.astype(str).flatten()]).encode()
+        ##print(s)
+        #print(dataset.PixelData[:20])
+        #print(len(dataset.PixelData))
+        #md5.update(dataset.PixelData)
+
+        #hash = md5.hexdigest()
+
+        hasher = blake3()
+        hasher.update(dataset.PixelData)
+        hash = hasher.hexdigest()
+        #dataset.PixelData
+
+        d = (
+            file.name,
+            study_desc,
+            instance_number,
+            patient_name,
+            series_desc,
+            slice_location,
+            hash,
+            series_instances_uid
+        )
+
+        #hasher = blake3()
+        #first = True
+        #for i in dataset.pixel_array.astype(str).flatten():
+        #    if first:
+        #        first = False
+        #        hasher.update(f"{i}".encode())
+        #    else:
+        #        hasher.update(f",{i}".encode())
+
+        #hash = hasher.digest()
+
+        #hash = get_file_hash(file, hasher="md5")
+
+        #hash = None  # If we don't use the hash...
+        self.file_detail_map[file] = d, hash, d2
+
+        return d, hash, d2
+
     def UpdateListCtrl(self, event=None):
         logger.debug("update list ctrl")
         self.list_ctrl.DeleteAllItems()
@@ -909,69 +1028,26 @@ class AnonGui(wx.App):
         self.series_map = defaultdict(list)
         self.series_map_details = defaultdict(dict)
 
+        hashes = []
+
         for n, f in enumerate(self.files):
             progress_dialog.Update(n)
             # dataset = pydicom.read_file(f)
 
             if f in self.file_detail_map:
                 d, hash, d2 = self.file_detail_map[f]
+                print("in map")
             else:
                 try:
                     dataset = pydicom.dcmread(f)
                 except FileNotFoundError:
                     return
 
-                try:
+                print("recalc")
-                    study_desc = dataset.StudyDescription
+                d, hash, d2 = self.add_datails_to_file_detail_map(dataset, f)
-                except:
-                    study_desc = "..."
-                try:
-                    series_desc = dataset.SeriesDescription
-                except:
-                    series_desc = "..."
-                try:
-                    instance_number = f"{dataset.InstanceNumber:03}"
-                except:
-                    instance_number = "..."
-                try:
-                    patient_name = str(dataset.PatientName)
-                except:
-                    patient_name = "..."
-                try:
-                    slice_location = str(dataset.SliceLocation)
-                except:
-                    slice_location = "..."
 
-                d = (
+            hashes.append(hash)
-                    f.name,
-                    study_desc,
-                    instance_number,
-                    patient_name,
-                    series_desc,
-                    slice_location,
-                )
 
-                series_instances_uid = str(dataset.SeriesInstanceUID)
-                d2 = {
-                    "series_instances_uid": series_instances_uid,
-                    "series_description": series_desc,
-                    "study_description": study_desc,
-                    "name": patient_name,
-                }
-
-                #md5 = hashlib.md5()
-                #first = True
-                #for i in dataset.pixel_array.astype(str).flatten():
-                #    if first:
-                #        first = False
-                #        md5.update(f"{i}".encode())
-                #    else:
-                #        md5.update(f",{i}".encode())
-
-                #hash = md5.hexdigest()
-
-                hash =  None # If we don't use the hash...
-                self.file_detail_map[f] = d, hash, d2
 
             series_instances_uid = d2["series_instances_uid"]
             try:
@@ -991,12 +1067,53 @@ class AnonGui(wx.App):
             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()
 
+        #if hashes:
+        #    self.check_image_hashes(hashes)
+
+    def check_image_hashes(self, evt):
+        if self.login_success and not self.image_hash_check_in_progress:
+            self.image_hash_check_in_progress = True
+
+            to_check = self.file_detail_map.keys() - self.file_duplicate_check.keys()
+            print(to_check)
+
+            if to_check:
+                hash_file_map = {}
+                for file in to_check:
+                    hash_file_map[self.file_detail_map[file][1]] = file
+
+                
+
+                hashes = list(hash_file_map.keys())
+
+                self.rqst.headers["X-CSRFToken"] = self.rqst.cookies["csrftoken"]
+                # print(self.rqst.headers)
+                # print(self.rqst.cookies)
+                resp = self.rqst.post(
+                    f"{self.base_site_url}/api/atlas/check_image_hashes/",
+                    data=json.dumps(hashes),
+                    #files=files,
+                )
+
+                for hash, dup in resp.json().items():
+                    self.file_duplicate_check[hash_file_map[hash]] = dup
+
+                print(self.file_duplicate_check)
+                wx.CallAfter(self.UpdateListCtrl)
+            self.image_hash_check_in_progress = False
+
     def OnColRightClick(self, event):
         item = self.list_ctrl.GetColumn(event.GetColumn())
         logger.debug(item)
@@ -1013,7 +1130,9 @@ class AnonGui(wx.App):
 
         # chunck files
         n = 10
-        chunked_files  = [files_to_upload[i:i + n] for i in range(0, len(files_to_upload), n)]
+        chunked_files = [
+            files_to_upload[i : i + n] for i in range(0, len(files_to_upload), n)
+        ]
 
         progress_dialog = wx.ProgressDialog(
             "Uploading files",
@@ -1029,10 +1148,10 @@ class AnonGui(wx.App):
 
             def upload_files(files):
                 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(
-                    f"{self.base_site_url}api/atlas/upload_dicom",
+                    f"{self.base_site_url}/api/atlas/upload_dicom",
                     # data=data,
                     files=files,
                 )
@@ -1041,8 +1160,6 @@ class AnonGui(wx.App):
                 logger.debug(f"{resp.content}")
                 return resp
 
-
-
             progress_dialog.Update(n, f"Uploading batch {n}/{len(chunked_files)}")
 
             logger.debug(f"n: {n}")
@@ -1052,7 +1169,6 @@ class AnonGui(wx.App):
                 upload_file_list.extend(resp.json()["uploaded"])
                 duplicate_file_list.extend(resp.json()["duplicates"])
 
-
                 continue
 
             logger.debug(f"n: {n} fail")
@@ -1068,11 +1184,15 @@ class AnonGui(wx.App):
         print(upload_file_list)
         print(duplicate_file_list)
 
-        wx.CallAfter(self.upload_complete_message, upload_file_list, duplicate_file_list)
+        wx.CallAfter(
-
+            self.upload_complete_message, upload_file_list, duplicate_file_list
+        )
 
     def upload_complete_message(self, upload_file_list, duplicate_file_list):
-        wx.MessageBox(f"Files uploaded: {len(upload_file_list)}\nDuplicate files (not uploaded): {len(duplicate_file_list)}")
+        wx.MessageBox(
+            f"Files uploaded: {len(upload_file_list)}\nDuplicate files (not uploaded): {len(duplicate_file_list)}"
+        )
+        self.file_duplicate_check = {}
 
     def OnDragInit(self, event):
         my_data = wx.FileDataObject()
@@ -1093,10 +1213,10 @@ 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,

wxDicomViewer.py

@@ -210,7 +210,7 @@ class ViewerFrame(wx.Frame):
             if self.loadCentered:
                 bmpX0 = (windowsize[0] - self.bitmap.Width) / 2
                 bmpY0 = (windowsize[1] - self.bitmap.Height) / 2
-            dc.DrawBitmap(self.bitmap, bmpX0, bmpY0, False)
+            dc.DrawBitmap(self.bitmap, int(bmpX0), int(bmpY0), False)
 
     # ------------------------------------------------------------
     #  ViewerFrame.ConvertWXToPIL()