Now can convert most images

.gitignore

@@ -165,3 +165,4 @@ cython_debug/
 # xfr
 *.xlsx
 *.local.txt
+*.nii.gz

src/pacs.py

@@ -50,7 +50,8 @@ def login(id=USER_ID, pw=PASSWORD):
     app = Application(backend="uia").start(r'C:\Users\xfr\Desktop\PACS.exe')
 
     w = Desktop(backend="uia").window(title_re='.* - Microsoft​ Edge$')
-    w.wait('ready')
+    w.wait('ready', timeout=30)
+
 
     # time.sleep(9)
 
@@ -88,7 +89,10 @@ def save_tag(window, outdir):
 
     TDicomTagListForm = window['DICOM 標籤清單Dialog']
     if TDicomTagListForm.exists():
+        try:
             TDicomTagListForm.close()
+        except Exception as e:
+            logging.critical(e, exc_info=True)  # log exception info at CRITICAL log level
         TDicomTagListForm.wait_not('exists', 30)
 
     TToolBar = window.child_window(class_name='TToolBar', found_index=2)
@@ -110,7 +114,7 @@ def save_tag(window, outdir):
     NEdit.wait('ready', 99)
     edit = NEdit.wrapper_object()
     pahtname = os.path.join(outdir, edit.get_value())
-    for p in glob.glob(pahtname + '*'):
+    for p in glob.glob(pahtname + '.*'):
         os.remove(p)
     edit.set_text(pahtname)
     dlg_save['存檔(S)Button'].wrapper_object().click()
@@ -156,7 +160,7 @@ def save_study(chartno, outdir, only_tag):
     c = series[0]
     c.set_focus()
     mouse_click(c)
-    keyboard.send_keys('^i')
+    keyboard.send_keys('^i') #隱藏標籤
 
     # logging.warning(str(TFlowPanel.get_properties()))
     # print(str(TFlowPanel.get_properties()))
@@ -168,6 +172,7 @@ def save_study(chartno, outdir, only_tag):
 
         logging.warning(str(c.element_info))
         # c.wait('ready') #AttributeError: 'UIAWrapper' object has no attribute 'wait'
+        keyboard.send_keys('{ESC}')
         c.set_focus()
 
         mouse_click(c)
@@ -338,10 +343,11 @@ def save_patient(chartno, outdir, query = "CT,MR", only_tag=False):
 
             time.sleep(.1)
 
+        # exit()
+
     logging.warning(chartno+" completed "+query)
     return 0
 
-        # exit()
  
 
 actionlogger.enable()
@@ -362,10 +368,12 @@ def main():
     # logger.handlers[0].setFormatter(formatter)
 
     app, window = login()
-    save_patient('5344141', r'T:\0\5344141', query="CT,MR")
+    # save_patient('5344141', r'T:\0\5344141', query="CT,MR")
     # save_patient('5344141', r'T:\0\5344141', query="CT")
     # save_patient('2380784', r'T:\3\2380784', query=False)
     # save_study('2380784', outdir=r'T:\0\2380784')
+    # save_patient('6631848', r'T:\0\6631848', query='MR')
+    save_patient('6166521', r'T:\0\6166521', query='CT,MR')
 
 
 

src/uni2nii.py

@@ -0,0 +1,481 @@
+
+import csv
+import itertools
+import os
+import re
+
+import struct
+
+import numpy as np
+import SimpleITK as sitk
+
+
+def get_image_size_imghdr(fname):
+    try:
+        with open(fname, 'rb') as fhandle:
+            head = fhandle.read(24)
+            if len(head) != 24:
+                return None
+            # if imghdr.what(fname) == 'jpeg':
+            if True:
+                try:
+                    fhandle.seek(0)
+                    size = 2
+                    ftype = 0
+                    while not 0xc0 <= ftype <= 0xcf:
+                        fhandle.seek(size, 1)
+                        byte = fhandle.read(1)
+                        while ord(byte) == 0xff:
+                            byte = fhandle.read(1)
+                        ftype = ord(byte)
+                        size = struct.unpack('>H', fhandle.read(2))[0] - 2
+                    fhandle.seek(1, 1)
+                    height, width = struct.unpack('>HH', fhandle.read(4))
+                    return width, height
+                except Exception:
+                    return None
+    except FileNotFoundError:
+        return "File not found"
+    except Exception as e:
+        return f"Error: {e}"
+
+
+class Series:
+    def __init__(self, root):
+        self.root = root
+        self.jpgs = {}
+        self.txts = []
+        self.headers = {}
+
+    def read_csv(file):
+        r = {}
+        with open(file, encoding="utf-8") as csvfile:
+            rows = csv.reader(csvfile)
+
+            for row in rows:
+                # print(row)
+                if len(row)>4:
+                    r[row[4]] = row[3]
+
+        return r
+
+
+    def sanitize_filename(filename: str, replacement: str = "_") -> str:
+        """
+        Remove invalid characters from a filename.
+        
+        Parameters:
+        - filename: The original filename
+        - replacement: Character to replace invalid ones with (default is "_")
+        
+        Returns:
+        - A sanitized version of the filename
+        """
+        # Define a regex pattern of invalid filename characters
+        # Windows invalid characters: \ / : * ? " < > |
+        invalid_chars = r'[\\/:*?"<>|]'
+        sanitized = re.sub(invalid_chars, replacement, filename)
+        
+        # Optionally, strip leading/trailing whitespace or dots
+        sanitized = sanitized.strip().strip(".")
+        
+        return sanitized
+
+    def add_txt(self, root, name):
+        # print(name)
+        p = os.path.join(root, name)
+        self.txts.append(p)
+        ins = int(name.split('_')[4][:-4])
+        r = Series.read_csv(p)
+        self.headers[ins] = r
+        # print(r['Image Position (Patient)'])
+        # print(r['Image Orientation (Patient)'])
+        # print(r)
+        # exit()
+
+
+
+       
+    def add_jpg(self, root, name):
+        ins = int(name.split('_')[4])
+        p = os.path.join(root, name)
+        size = get_image_size_imghdr(p)
+        if size not in self.jpgs:
+            self.jpgs[size] = {}
+        # print(size, p)
+        self.jpgs[size][ins] = p
+
+    def write_pairs(self, pair, value, outdir):
+        a, b = pair
+        norm1, size1 = value
+
+        # print(size1)
+
+        # print(self.jpgs.keys())
+        # k, v = sorted(self.jpgs.items(), key=lambda item: -len(item[1]))[0]
+        # print(k)
+
+        v = self.jpgs[size1]
+        fileNames = []
+        for ins in sorted(v.keys()):
+            # print(get_image_size_imghdr(v[ins]))
+            fileNames.append(v[ins])
+
+        # fileNames = []
+        # for ins in sorted(self.jpgs.keys()):
+        #     print(get_image_size_imghdr(self.jpgs[ins]))
+        #     fileNames.append(self.jpgs[ins])
+
+        image = sitk.ReadImage(fileNames)
+
+        i0 = sitk.VectorIndexSelectionCast(image, 0)
+        i1 = sitk.VectorIndexSelectionCast(image, 1)
+        i2 = sitk.VectorIndexSelectionCast(image, 2)
+
+        image = i0
+
+        # print(image)
+
+        # keys = sorted(self.headers.keys())
+        # a = keys[0]
+        # b = keys[-1]
+        # print(self.headers[a]['Image Position (Patient)'])
+        # print(self.headers[a]['Image Orientation (Patient)'])
+        # print(self.headers[b]['Image Position (Patient)'])
+        # print(self.headers[b]['Image Orientation (Patient)'])
+
+
+        # if "Image Orientation (Patient)" not in self.headers[a]:
+        #     print('skip due to no "Image Orientation (Patient)"')
+        #     return
+
+        Orientation = np.array([float(p) for p in self.headers[a]['Image Orientation (Patient)'].split('\\')])
+        Spacing = np.array([float(p) for p in self.headers[a]['Pixel Spacing'].split('\\')])
+
+        p1 = np.array([float(p) for p in self.headers[a]['Image Position (Patient)'].split('\\')])
+        p2 = np.array([float(p) for p in self.headers[b]['Image Position (Patient)'].split('\\')])
+
+        diff_pos = (p2-p1)/(b-a)
+        norm = np.linalg.norm(diff_pos)
+        # print(p1)
+        # print(p2)
+        # print(norm)
+
+        if norm < 0.1:
+            print('skip due to small norm', norm)
+            return
+
+        unit_vec = diff_pos / norm
+
+        # print(unit_vec)
+        # print(Orientation)
+
+        o0 = Orientation[:3]
+        o1 = Orientation[3:]
+        # print(np.cross(o0, o1))
+
+        d = np.concatenate([Orientation, unit_vec])
+        # d = np.concatenate([o1, o0, unit_vec])
+        # d = np.concatenate([o1, unit_vec, o0])
+        d = np.linalg.inv(d.reshape(3,3)).flatten()
+        s = np.append(Spacing, norm)
+
+        image.SetDirection(d)
+        image.SetOrigin(p1)
+        image.SetSpacing(s)
+
+
+        # print(image)
+        # print(d)
+        # print(s)
+
+        date = self.headers[a]["Study Date"].strip()
+
+        name = '%s-%s-%s.nii.gz' % (date, self.headers[a]['Series Number'].strip(), self.headers[a]['Series Description'].strip())
+        sitk.WriteImage(image, os.path.join(outdir, Series.sanitize_filename(name)))
+
+
+    def write_single(self, a, outdir):
+        fileNames = []
+        for ins in sorted(self.jpgs.keys()):
+            fileNames.append(self.jpgs[ins])
+
+        image = sitk.ReadImage(fileNames)
+
+        i0 = sitk.VectorIndexSelectionCast(image, 0)
+        i1 = sitk.VectorIndexSelectionCast(image, 1)
+        i2 = sitk.VectorIndexSelectionCast(image, 2)
+
+        image = i0
+
+        Orientation = np.array([float(p) for p in self.headers[a]['Image Orientation (Patient)'].split('\\')])
+        Spacing = np.array([float(p) for p in self.headers[a]['Pixel Spacing'].split('\\')])
+
+        o0 = Orientation[:3]
+        o1 = Orientation[3:]
+        unit_vec = np.cross(o0, o1)
+
+        d = np.concatenate([Orientation, unit_vec])
+        d = np.linalg.inv(d.reshape(3,3)).flatten()
+
+        print(Orientation)
+        print(d)
+
+        p1 = np.array([float(p) for p in self.headers[a]['Image Position (Patient)'].split('\\')])
+
+        norm = float(self.headers[a]["Slice Thickness"])
+        s = np.append(Spacing, norm)
+
+        image.SetDirection(d)
+        image.SetOrigin(p1)
+        image.SetSpacing(s)
+
+
+        # print(image)
+        # print(d)
+        # print(s)
+
+        name = '%s-%d-%s.nii.gz' % (self.headers[a]['Series Number'].strip(), a, self.headers[a]['Series Description'].strip())
+        # print(name)
+        sitk.WriteImage(image, os.path.join(outdir, Series.sanitize_filename(name)))
+
+        return
+
+        exit()
+
+
+
+
+        p1 = np.array([float(p) for p in self.headers[a]['Image Position (Patient)'].split('\\')])
+        p2 = np.array([float(p) for p in self.headers[b]['Image Position (Patient)'].split('\\')])
+
+        diff_pos = (p2-p1)/(b-a)
+        norm = np.linalg.norm(diff_pos)
+        print(p1)
+        print(p2)
+        print(norm)
+
+        if norm < 0.1:
+            print('skip due to small norm', norm)
+            return
+
+        unit_vec = diff_pos / norm
+
+        print(unit_vec)
+        print(Orientation)
+
+        o0 = Orientation[:3]
+        o1 = Orientation[3:]
+        # print(np.cross(o0, o1))
+
+        d = np.concatenate([Orientation, unit_vec])
+        # d = np.concatenate([o1, o0, unit_vec])
+        # d = np.concatenate([o1, unit_vec, o0])
+        d = np.linalg.inv(d.reshape(3,3)).flatten()
+        s = np.append(Spacing, norm)
+
+        image.SetDirection(d)
+        image.SetOrigin(p1)
+        image.SetSpacing(s)
+
+
+        # print(image)
+        # print(d)
+        # print(s)
+
+        name = '%s-%s.nii.gz' % (self.headers[a]['Series Number'].strip(), self.headers[a]['Series Description'].strip())
+        sitk.WriteImage(image, os.path.join(outdir, Series.sanitize_filename(name)))
+
+
+
+    def write(self, outdir):
+
+        # if len(self.jpgs)<9:
+        #     return
+
+        valid_keys = []
+        
+        pairs = {}
+
+
+        for k in sorted(self.headers.keys()):
+            header = self.headers[k]
+            if "Image Orientation (Patient)" not in header:
+                continue
+            valid_keys.append(k)
+
+        # print(valid_keys)
+        # exit()
+
+        if not valid_keys:
+            return
+
+        a = valid_keys[0]
+        name = '%s-%s.nii.gz' % (self.headers[a]['Series Number'].strip(), self.headers[a]['Series Description'].strip())
+        # print(name, valid_keys)
+
+        if len(valid_keys) > 1:
+            for c in itertools.combinations(valid_keys, 2):
+                a, b = c
+
+                size1 = int(self.headers[a]["Columns"]),int(self.headers[a]["Rows"])
+                size2 = int(self.headers[b]["Columns"]),int(self.headers[b]["Rows"])
+                if size1 != size2:
+                    continue
+
+                o1 = np.array([float(o) for o in self.headers[a]["Image Orientation (Patient)"].split('\\')])
+                cr1 = np.cross(o1[:3], o1[3:])
+                o2 = np.array([float(o) for o in self.headers[b]["Image Orientation (Patient)"].split('\\')])
+                cr2 = np.cross(o2[:3], o2[3:])
+                dot = np.dot(cr1, cr2)
+                if dot < -0.9:
+                    pass
+                elif dot > 0.9:
+                    p1 = np.array([float(o) for o in self.headers[a]["Image Position (Patient)"].split('\\')])
+                    p2 = np.array([float(o) for o in self.headers[b]["Image Position (Patient)"].split('\\')])
+                    pairs[c] = np.linalg.norm(p2-p1), size1
+                # else:
+                #     print(a, o1)
+                #     print(b, o2)
+                # print(c, dot)
+
+        if pairs:
+            for k, v in pairs.items():
+                # continue
+                print(name, k, v)
+                self.write_pairs(k, v, outdir)
+                break
+        # else:
+        #     for k in valid_keys:
+        #         self.write_single(k, outdir)
+
+        return
+
+        fileNames = []
+        for ins in sorted(self.jpgs.keys()):
+            fileNames.append(self.jpgs[ins])
+
+        image = sitk.ReadImage(fileNames)
+
+        i0 = sitk.VectorIndexSelectionCast(image, 0)
+        i1 = sitk.VectorIndexSelectionCast(image, 1)
+        i2 = sitk.VectorIndexSelectionCast(image, 2)
+
+        image = i0
+
+        # print(image)
+
+        keys = sorted(self.headers.keys())
+        a = keys[0]
+        b = keys[-1]
+        # print(self.headers[a]['Image Position (Patient)'])
+        # print(self.headers[a]['Image Orientation (Patient)'])
+        # print(self.headers[b]['Image Position (Patient)'])
+        # print(self.headers[b]['Image Orientation (Patient)'])
+
+
+        if "Image Orientation (Patient)" not in self.headers[a]:
+            print('skip due to no "Image Orientation (Patient)"')
+            return
+
+        Orientation = np.array([float(p) for p in self.headers[a]['Image Orientation (Patient)'].split('\\')])
+        Spacing = np.array([float(p) for p in self.headers[a]['Pixel Spacing'].split('\\')])
+
+        p1 = np.array([float(p) for p in self.headers[a]['Image Position (Patient)'].split('\\')])
+        p2 = np.array([float(p) for p in self.headers[b]['Image Position (Patient)'].split('\\')])
+
+        diff_pos = (p2-p1)/(b-a)
+        norm = np.linalg.norm(diff_pos)
+        print(p1)
+        print(p2)
+        print(norm)
+
+        if norm < 0.1:
+            print('skip due to small norm', norm)
+            return
+
+        unit_vec = diff_pos / norm
+
+        print(unit_vec)
+        print(Orientation)
+
+        o0 = Orientation[:3]
+        o1 = Orientation[3:]
+        # print(np.cross(o0, o1))
+
+        d = np.concatenate([Orientation, unit_vec])
+        # d = np.concatenate([o1, o0, unit_vec])
+        # d = np.concatenate([o1, unit_vec, o0])
+        d = np.linalg.inv(d.reshape(3,3)).flatten()
+        s = np.append(Spacing, norm)
+
+        image.SetDirection(d)
+        image.SetOrigin(p1)
+        image.SetSpacing(s)
+
+
+        # print(image)
+        # print(d)
+        # print(s)
+
+        sitk.WriteImage(image, os.path.join(outdir, Series.sanitize_filename(name)))
+
+
+    def dump(self):
+        # for f in self.jpgs:
+        #     print(f)
+        # print(len(self.jpgs))
+        for f in self.txts:
+            print(f)
+        print(len(self.jpgs), len(self.txts))
+
+
+class Study:
+    def __init__(self, indir):
+        self.root = indir
+        self.series = {}
+
+        for root, dirs, files in os.walk(self.root):
+            for name in files:
+                series_num = int(name.split('_')[3])
+                if series_num not in self.series:
+                    self.series[series_num] = Series(root)
+                if name.endswith('.jpg'):
+                    self.series[series_num].add_jpg(root, name)
+                if name.endswith('.txt'):
+                    self.series[series_num].add_txt(root, name)
+                    # series[series_num].txts.append(os.path.join(root, name))
+
+    def write(self, outdir):
+        os.makedirs(outdir, exist_ok=True)
+        for k in sorted(self.series.keys()):
+            # if k != 3:
+            #     continue
+            self.series[k].write(outdir)
+
+
+# "Protocol Name"
+                
+
+
+def main():
+
+    # s = Study(r'T:\0\6166521\20250513_MR_2316')
+    # s = Study(r'T:\0\6166521\20220330_MR_1690')
+    # s = Study(r'T:\0\6166521\20210625_MR_693')
+    # s = Study(r'T:\0\6166521\20231117_MR_1983')
+    # s.write('0/')
+    # exit()
+
+    for e in os.scandir(r'T:\0\6166521'):
+        if e.is_dir():
+            indir = e.path
+            outdir = os.path.join('0/', e.name)
+            print(indir)
+            # continue
+            s = Study(indir)
+            s.write(outdir)
+
+
+if __name__ == '__main__':
+    main()