keep partial study

src/list-pituitary.py

@@ -0,0 +1,52 @@
+
+from pathlib import Path
+
+import base64
+import hashlib
+import datetime
+import logging
+
+import pandas as pd
+
+def hashptid(mrn, hosp='NTUH'):
+
+    ptsalt = (mrn+hosp).upper().encode()
+    hash_in_bytes = hashlib.md5(ptsalt)
+
+    md5  = hash_in_bytes.hexdigest()
+    hash = base64.b32encode(hash_in_bytes.digest())[:8].decode()
+
+
+    # hash32 = base64.b32encode(hash_in_bytes)[:8].decode()
+    # hash10 = str(int(hashlib.md5(ptsalt).hexdigest(), 16))[-8:]
+
+    return md5, hash
+
+
+  
+
+def main():
+    FORMAT = '%(asctime)s %(message)s'
+    logging.basicConfig(filename=__file__.replace('.py','.%s.log'%str(datetime.datetime.now()).replace(':','')), 
+                        format=FORMAT)
+
+    # df = pd.read_excel('pituitary-op.xlsx')
+    # series = df['PatChartNo'].drop_duplicates().iloc[-1000:].iloc[::-1]
+    # outdir = r'T:\pituitary-op'
+
+    df = pd.read_excel('pituitary-srs.xlsx', sheet_name='NFA Data (n=178)', header=1)
+    series = df[~df['Patient ID'].isna()]['Patient ID'].drop_duplicates()
+
+    for index, row in series.items():
+        if isinstance(row, float):
+            row = int(row)
+        chartno = str(int(row)).zfill(7)
+        md5, hash = hashptid(chartno)
+
+        print(chartno, hash)
+
+    return 0
+
+
+if __name__ == '__main__':
+    main()

src/pacs.py

@@ -1,4 +1,6 @@
 
+from pathlib import Path
+
 import datetime
 import glob
 import logging
@@ -18,7 +20,7 @@ def mouse_click(ws):
     mouse.move(coords=coords)
     time.sleep(0.1)
     mouse.click(coords=coords)
-    time.sleep(0.2)
+    time.sleep(0.1)
     # mouse.press(coords=coords)
     # mouse.release(coords=coords)
 
@@ -78,13 +80,20 @@ def dump(pane):
     print(pane.print_control_identifiers())
     # print(len(pane.children()))
 
+# TDicomTagListForm = None
 
 def save_tag(window, outdir):
+    global TDicomTagListForm
     mouse_click(window['註釋／標籤'])
-    TToolBar = window.child_window(class_name='TToolBar', found_index=2)
 
+    TDicomTagListForm = window['DICOM 標籤清單Dialog']
+    if TDicomTagListForm.exists():
+        TDicomTagListForm.close()
+        TDicomTagListForm.wait_not('exists', 20)
+
+    TToolBar = window.child_window(class_name='TToolBar', found_index=2)
     Button5 = TToolBar.Button5
-    Button5.wait('ready', 9)
+    Button5.wait('ready', 10)
     # time.sleep(2)
     mouse_click(Button5)
 
@@ -93,6 +102,7 @@ def save_tag(window, outdir):
     export = export_to_file.wrapper_object()
     export.click()
 
+
     TDicomTagListForm = window['DICOM 標籤清單Dialog']
 
     dlg_save = Desktop(backend="uia").window(title='另存新檔')
@@ -106,7 +116,9 @@ def save_tag(window, outdir):
     dlg_save['存檔(S)Button'].wrapper_object().click()
 
     TDicomTagListForm.close()
-    TDicomTagListForm.wait_not('exists', 9)
+    # logging.warning("TDicomTagListForm closing")
+    # TDicomTagListForm.wait_not('exists', 60)
+    # logging.warning("TDicomTagListForm not exists")
 
     return pahtname
 
@@ -123,7 +135,10 @@ def save_study(chartno, outdir, only_tag):
     #         time.sleep(1)
 
     logging.warning('connecting '+chartno)
-    app = Application(backend="uia").connect(title_re='^%s.*'%chartno, timeout=200)
+    app = Application(backend="uia").connect(title_re='.*%s.*'%chartno, timeout=200)
+
+    shutil.rmtree(outdir, ignore_errors=True)
+    os.makedirs(outdir, exist_ok=True)
 
     logging.warning(str(app))
     window = app.top_window()
@@ -152,16 +167,17 @@ def save_study(chartno, outdir, only_tag):
     for c in series:
 
         logging.warning(str(c.element_info))
+        # c.wait('ready') #AttributeError: 'UIAWrapper' object has no attribute 'wait'
         c.set_focus()
 
         mouse_click(c)
         keyboard.send_keys('^{HOME}')
-        time.sleep(1)
+        time.sleep(.1)
         p = save_tag(window, outdir)
 
         mouse_click(c)
         keyboard.send_keys('^{END}')
-        time.sleep(1)
+        time.sleep(.1)
         p = save_tag(window, outdir)
 
         # mouse_click(c)
@@ -180,6 +196,7 @@ def save_study(chartno, outdir, only_tag):
         # logging.warning(str(datetime.datetime.now()))
         TFormSaveBitmap = window['選項']
         # TFormSaveBitmap.dump_tree(filename='z-%s-TFormSaveBitmap.txt'%chartno)
+        TFormSaveBitmap.wait('ready')
 
         Edit5 = TFormSaveBitmap.Edit5
         Edit5.wait('ready')
@@ -189,7 +206,7 @@ def save_study(chartno, outdir, only_tag):
         TFormSaveBitmap.Button2.click()
 
         logging.warning('button clicked')
-        time.sleep(1)
+        time.sleep(.1)
         logging.warning('saving started')
         saving = window.child_window(title_re='^另存新檔.*')
         logging.warning('saving exists')
@@ -199,6 +216,7 @@ def save_study(chartno, outdir, only_tag):
     c.set_focus()
     mouse_click(c)
     keyboard.send_keys('^q')
+    # window.wait_not('exists', 9)
 
     # while True:
     #     try:
@@ -242,25 +260,68 @@ def save_patient(chartno, outdir, query = "CT,MR", only_tag=False):
           
     ListView = ListItem.parent()
 
-    shutil.rmtree(outdir, ignore_errors=True)
-    os.makedirs(outdir, exist_ok=True)
+    # shutil.rmtree(outdir, ignore_errors=True)
+    # os.makedirs(outdir, exist_ok=True)
 
     items =[]
 
+    rows = []
+    row = None
+
+    LeftUpper = ListView.items()[0]
+    mouse_click(LeftUpper)
+
     for item in ListView.items():
-        if item.texts()[0] != '開啟影像':
-            continue
-        items.append(item)
-        logging.debug(str(item.rectangle()))      
+        # logging.warning(str(item))
+        # logging.warning(str(dir(item)))
+        # logging.warning(str(item.texts()))
+
+        if item.texts()[0] == '開啟影像':
+            if row:
+                rows.append(row)
+                # logging.warning(str(row))
+            items.append(item)
+            row = []
+
+        if row is not None:
+            row.append(item.texts()[0])
+
+        # if item.texts()[0] != '開啟影像':
+        #     continue
+        # items.append(item)
+        # logging.debug(str(item.rectangle()))
+
+    rows.append(row)
+    # logging.warning(str(row))
+
+    # logging.warning(str(len(items)))
+    # logging.warning(str(items))
+
+    # exit()
 
     for i, item in enumerate(items):
-        # if i < 7:
-        #     continue
+
+        series_name = '%s_%s_%s' % (rows[i][5], rows[i][9], rows[i][10])
+        series_name = series_name.replace('/', '').replace(' ', '')
+        complete_file = Path(f'{outdir}\\{series_name}.complete')
+
+        if complete_file.is_file():
+            logging.warning('skip '+str(complete_file))
+        else:
+
+            subdir = Path(f'{outdir}\\{series_name}')
+
+            time.sleep(.1)
+            logging.warning(str(item.get_properties()))
+            mouse_click(item)
+
+            save_study(chartno, subdir, only_tag)
+            complete_file.touch()
+
         bottom = False
         logging.warning(str(items[i].rectangle()))      
-
         try:
-            if items[i+1].rectangle().top < 1:
+            if items[i+2].rectangle().top < 1:
                bottom = True
         except:
             bottom = True
@@ -275,14 +336,8 @@ def save_patient(chartno, outdir, query = "CT,MR", only_tag=False):
             # coords = (r.left + r.right)//2, (r.top + r.bottom)//2
             # mouse.scroll(coords=coords)
 
-            time.sleep(2)
+            time.sleep(.1)
 
-        # item.wait('ready') # no attribute wait
-        time.sleep(1)
-        logging.warning(str(item.get_properties()))
-        mouse_click(item)
-
-        save_study(chartno, outdir, only_tag)
     logging.warning(chartno+" completed "+query)
     return 0
 

src/pituitary.py

@@ -22,7 +22,9 @@ def get_pacs(series, outdir, max_patients=100):
             continue
 
         logging.warning('saving '+chartno)
-        pacs.save_patient(chartno, f'{outdir}\\{chartno}', query="CT,MR", only_tag=True)
+        pacs.save_patient(chartno, f'{outdir}\\{chartno}', query="CT,MR", 
+                        #   only_tag=True
+                          )
         
         complete_file.touch()
         num_patients += 1