Now can convert most images
This commit is contained in:
parent
7581a7cb16
commit
283748aa78
3 changed files with 497 additions and 7 deletions
3
.gitignore
vendored
3
.gitignore
vendored
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@ -164,4 +164,5 @@ cython_debug/
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# xfr
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*.xlsx
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*.local.txt
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*.local.txt
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*.nii.gz
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20
src/pacs.py
20
src/pacs.py
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@ -50,7 +50,8 @@ def login(id=USER_ID, pw=PASSWORD):
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app = Application(backend="uia").start(r'C:\Users\xfr\Desktop\PACS.exe')
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w = Desktop(backend="uia").window(title_re='.* - Microsoft Edge$')
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w.wait('ready')
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w.wait('ready', timeout=30)
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# time.sleep(9)
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@ -88,7 +89,10 @@ def save_tag(window, outdir):
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TDicomTagListForm = window['DICOM 標籤清單Dialog']
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if TDicomTagListForm.exists():
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TDicomTagListForm.close()
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try:
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TDicomTagListForm.close()
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except Exception as e:
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logging.critical(e, exc_info=True) # log exception info at CRITICAL log level
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TDicomTagListForm.wait_not('exists', 30)
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TToolBar = window.child_window(class_name='TToolBar', found_index=2)
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@ -110,7 +114,7 @@ def save_tag(window, outdir):
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NEdit.wait('ready', 99)
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edit = NEdit.wrapper_object()
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pahtname = os.path.join(outdir, edit.get_value())
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for p in glob.glob(pahtname + '*'):
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for p in glob.glob(pahtname + '.*'):
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os.remove(p)
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edit.set_text(pahtname)
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dlg_save['存檔(S)Button'].wrapper_object().click()
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@ -156,7 +160,7 @@ def save_study(chartno, outdir, only_tag):
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c = series[0]
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c.set_focus()
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mouse_click(c)
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keyboard.send_keys('^i')
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keyboard.send_keys('^i') #隱藏標籤
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# logging.warning(str(TFlowPanel.get_properties()))
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# print(str(TFlowPanel.get_properties()))
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@ -168,6 +172,7 @@ def save_study(chartno, outdir, only_tag):
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logging.warning(str(c.element_info))
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# c.wait('ready') #AttributeError: 'UIAWrapper' object has no attribute 'wait'
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keyboard.send_keys('{ESC}')
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c.set_focus()
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mouse_click(c)
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@ -338,10 +343,11 @@ def save_patient(chartno, outdir, query = "CT,MR", only_tag=False):
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time.sleep(.1)
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# exit()
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logging.warning(chartno+" completed "+query)
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return 0
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# exit()
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actionlogger.enable()
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@ -362,10 +368,12 @@ def main():
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# logger.handlers[0].setFormatter(formatter)
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app, window = login()
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save_patient('5344141', r'T:\0\5344141', query="CT,MR")
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# save_patient('5344141', r'T:\0\5344141', query="CT,MR")
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# save_patient('5344141', r'T:\0\5344141', query="CT")
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# save_patient('2380784', r'T:\3\2380784', query=False)
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# save_study('2380784', outdir=r'T:\0\2380784')
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# save_patient('6631848', r'T:\0\6631848', query='MR')
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save_patient('6166521', r'T:\0\6166521', query='CT,MR')
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481
src/uni2nii.py
Normal file
481
src/uni2nii.py
Normal file
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@ -0,0 +1,481 @@
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import csv
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import itertools
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import os
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import re
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import struct
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import numpy as np
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import SimpleITK as sitk
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def get_image_size_imghdr(fname):
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try:
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with open(fname, 'rb') as fhandle:
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head = fhandle.read(24)
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if len(head) != 24:
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return None
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# if imghdr.what(fname) == 'jpeg':
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if True:
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try:
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fhandle.seek(0)
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size = 2
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ftype = 0
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while not 0xc0 <= ftype <= 0xcf:
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fhandle.seek(size, 1)
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byte = fhandle.read(1)
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while ord(byte) == 0xff:
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byte = fhandle.read(1)
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ftype = ord(byte)
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size = struct.unpack('>H', fhandle.read(2))[0] - 2
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fhandle.seek(1, 1)
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height, width = struct.unpack('>HH', fhandle.read(4))
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return width, height
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except Exception:
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return None
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except FileNotFoundError:
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return "File not found"
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except Exception as e:
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return f"Error: {e}"
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class Series:
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def __init__(self, root):
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self.root = root
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self.jpgs = {}
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self.txts = []
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self.headers = {}
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def read_csv(file):
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r = {}
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with open(file, encoding="utf-8") as csvfile:
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rows = csv.reader(csvfile)
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for row in rows:
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# print(row)
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if len(row)>4:
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r[row[4]] = row[3]
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return r
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def sanitize_filename(filename: str, replacement: str = "_") -> str:
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"""
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Remove invalid characters from a filename.
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Parameters:
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- filename: The original filename
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- replacement: Character to replace invalid ones with (default is "_")
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Returns:
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- A sanitized version of the filename
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"""
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# Define a regex pattern of invalid filename characters
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# Windows invalid characters: \ / : * ? " < > |
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invalid_chars = r'[\\/:*?"<>|]'
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sanitized = re.sub(invalid_chars, replacement, filename)
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# Optionally, strip leading/trailing whitespace or dots
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sanitized = sanitized.strip().strip(".")
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return sanitized
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def add_txt(self, root, name):
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# print(name)
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p = os.path.join(root, name)
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self.txts.append(p)
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ins = int(name.split('_')[4][:-4])
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r = Series.read_csv(p)
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self.headers[ins] = r
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# print(r['Image Position (Patient)'])
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# print(r['Image Orientation (Patient)'])
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# print(r)
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# exit()
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def add_jpg(self, root, name):
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ins = int(name.split('_')[4])
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p = os.path.join(root, name)
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size = get_image_size_imghdr(p)
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if size not in self.jpgs:
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self.jpgs[size] = {}
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# print(size, p)
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self.jpgs[size][ins] = p
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def write_pairs(self, pair, value, outdir):
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a, b = pair
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norm1, size1 = value
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# print(size1)
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# print(self.jpgs.keys())
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# k, v = sorted(self.jpgs.items(), key=lambda item: -len(item[1]))[0]
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# print(k)
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v = self.jpgs[size1]
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fileNames = []
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for ins in sorted(v.keys()):
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# print(get_image_size_imghdr(v[ins]))
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fileNames.append(v[ins])
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# fileNames = []
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# for ins in sorted(self.jpgs.keys()):
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# print(get_image_size_imghdr(self.jpgs[ins]))
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# fileNames.append(self.jpgs[ins])
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image = sitk.ReadImage(fileNames)
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i0 = sitk.VectorIndexSelectionCast(image, 0)
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i1 = sitk.VectorIndexSelectionCast(image, 1)
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i2 = sitk.VectorIndexSelectionCast(image, 2)
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image = i0
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# print(image)
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# keys = sorted(self.headers.keys())
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# a = keys[0]
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# b = keys[-1]
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# print(self.headers[a]['Image Position (Patient)'])
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# print(self.headers[a]['Image Orientation (Patient)'])
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# print(self.headers[b]['Image Position (Patient)'])
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# print(self.headers[b]['Image Orientation (Patient)'])
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# if "Image Orientation (Patient)" not in self.headers[a]:
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# print('skip due to no "Image Orientation (Patient)"')
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# return
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Orientation = np.array([float(p) for p in self.headers[a]['Image Orientation (Patient)'].split('\\')])
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Spacing = np.array([float(p) for p in self.headers[a]['Pixel Spacing'].split('\\')])
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p1 = np.array([float(p) for p in self.headers[a]['Image Position (Patient)'].split('\\')])
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p2 = np.array([float(p) for p in self.headers[b]['Image Position (Patient)'].split('\\')])
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diff_pos = (p2-p1)/(b-a)
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norm = np.linalg.norm(diff_pos)
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# print(p1)
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# print(p2)
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# print(norm)
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if norm < 0.1:
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print('skip due to small norm', norm)
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return
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unit_vec = diff_pos / norm
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# print(unit_vec)
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# print(Orientation)
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o0 = Orientation[:3]
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o1 = Orientation[3:]
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# print(np.cross(o0, o1))
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d = np.concatenate([Orientation, unit_vec])
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# d = np.concatenate([o1, o0, unit_vec])
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# d = np.concatenate([o1, unit_vec, o0])
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d = np.linalg.inv(d.reshape(3,3)).flatten()
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s = np.append(Spacing, norm)
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image.SetDirection(d)
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image.SetOrigin(p1)
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image.SetSpacing(s)
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# print(image)
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# print(d)
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# print(s)
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date = self.headers[a]["Study Date"].strip()
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name = '%s-%s-%s.nii.gz' % (date, self.headers[a]['Series Number'].strip(), self.headers[a]['Series Description'].strip())
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sitk.WriteImage(image, os.path.join(outdir, Series.sanitize_filename(name)))
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def write_single(self, a, outdir):
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fileNames = []
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for ins in sorted(self.jpgs.keys()):
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fileNames.append(self.jpgs[ins])
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image = sitk.ReadImage(fileNames)
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i0 = sitk.VectorIndexSelectionCast(image, 0)
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i1 = sitk.VectorIndexSelectionCast(image, 1)
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i2 = sitk.VectorIndexSelectionCast(image, 2)
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image = i0
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Orientation = np.array([float(p) for p in self.headers[a]['Image Orientation (Patient)'].split('\\')])
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Spacing = np.array([float(p) for p in self.headers[a]['Pixel Spacing'].split('\\')])
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o0 = Orientation[:3]
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o1 = Orientation[3:]
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unit_vec = np.cross(o0, o1)
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d = np.concatenate([Orientation, unit_vec])
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d = np.linalg.inv(d.reshape(3,3)).flatten()
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print(Orientation)
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print(d)
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p1 = np.array([float(p) for p in self.headers[a]['Image Position (Patient)'].split('\\')])
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norm = float(self.headers[a]["Slice Thickness"])
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s = np.append(Spacing, norm)
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image.SetDirection(d)
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image.SetOrigin(p1)
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image.SetSpacing(s)
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# print(image)
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# print(d)
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# print(s)
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name = '%s-%d-%s.nii.gz' % (self.headers[a]['Series Number'].strip(), a, self.headers[a]['Series Description'].strip())
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# print(name)
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sitk.WriteImage(image, os.path.join(outdir, Series.sanitize_filename(name)))
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return
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exit()
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p1 = np.array([float(p) for p in self.headers[a]['Image Position (Patient)'].split('\\')])
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p2 = np.array([float(p) for p in self.headers[b]['Image Position (Patient)'].split('\\')])
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diff_pos = (p2-p1)/(b-a)
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norm = np.linalg.norm(diff_pos)
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print(p1)
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print(p2)
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print(norm)
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if norm < 0.1:
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print('skip due to small norm', norm)
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return
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unit_vec = diff_pos / norm
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print(unit_vec)
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print(Orientation)
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o0 = Orientation[:3]
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o1 = Orientation[3:]
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# print(np.cross(o0, o1))
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d = np.concatenate([Orientation, unit_vec])
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# d = np.concatenate([o1, o0, unit_vec])
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# d = np.concatenate([o1, unit_vec, o0])
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d = np.linalg.inv(d.reshape(3,3)).flatten()
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s = np.append(Spacing, norm)
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image.SetDirection(d)
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image.SetOrigin(p1)
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image.SetSpacing(s)
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# print(image)
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# print(d)
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# print(s)
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name = '%s-%s.nii.gz' % (self.headers[a]['Series Number'].strip(), self.headers[a]['Series Description'].strip())
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sitk.WriteImage(image, os.path.join(outdir, Series.sanitize_filename(name)))
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def write(self, outdir):
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# if len(self.jpgs)<9:
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# return
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valid_keys = []
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pairs = {}
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for k in sorted(self.headers.keys()):
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header = self.headers[k]
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if "Image Orientation (Patient)" not in header:
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continue
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valid_keys.append(k)
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# print(valid_keys)
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# exit()
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if not valid_keys:
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return
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a = valid_keys[0]
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name = '%s-%s.nii.gz' % (self.headers[a]['Series Number'].strip(), self.headers[a]['Series Description'].strip())
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# print(name, valid_keys)
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if len(valid_keys) > 1:
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for c in itertools.combinations(valid_keys, 2):
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a, b = c
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size1 = int(self.headers[a]["Columns"]),int(self.headers[a]["Rows"])
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size2 = int(self.headers[b]["Columns"]),int(self.headers[b]["Rows"])
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if size1 != size2:
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continue
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o1 = np.array([float(o) for o in self.headers[a]["Image Orientation (Patient)"].split('\\')])
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cr1 = np.cross(o1[:3], o1[3:])
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o2 = np.array([float(o) for o in self.headers[b]["Image Orientation (Patient)"].split('\\')])
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cr2 = np.cross(o2[:3], o2[3:])
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dot = np.dot(cr1, cr2)
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if dot < -0.9:
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pass
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elif dot > 0.9:
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p1 = np.array([float(o) for o in self.headers[a]["Image Position (Patient)"].split('\\')])
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p2 = np.array([float(o) for o in self.headers[b]["Image Position (Patient)"].split('\\')])
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pairs[c] = np.linalg.norm(p2-p1), size1
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# else:
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# print(a, o1)
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# print(b, o2)
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# print(c, dot)
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if pairs:
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for k, v in pairs.items():
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# continue
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print(name, k, v)
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self.write_pairs(k, v, outdir)
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break
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# else:
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# for k in valid_keys:
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# self.write_single(k, outdir)
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return
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fileNames = []
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for ins in sorted(self.jpgs.keys()):
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fileNames.append(self.jpgs[ins])
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image = sitk.ReadImage(fileNames)
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i0 = sitk.VectorIndexSelectionCast(image, 0)
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i1 = sitk.VectorIndexSelectionCast(image, 1)
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i2 = sitk.VectorIndexSelectionCast(image, 2)
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image = i0
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# print(image)
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keys = sorted(self.headers.keys())
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a = keys[0]
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b = keys[-1]
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# print(self.headers[a]['Image Position (Patient)'])
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# print(self.headers[a]['Image Orientation (Patient)'])
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# print(self.headers[b]['Image Position (Patient)'])
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# print(self.headers[b]['Image Orientation (Patient)'])
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if "Image Orientation (Patient)" not in self.headers[a]:
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print('skip due to no "Image Orientation (Patient)"')
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return
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Orientation = np.array([float(p) for p in self.headers[a]['Image Orientation (Patient)'].split('\\')])
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Spacing = np.array([float(p) for p in self.headers[a]['Pixel Spacing'].split('\\')])
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p1 = np.array([float(p) for p in self.headers[a]['Image Position (Patient)'].split('\\')])
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p2 = np.array([float(p) for p in self.headers[b]['Image Position (Patient)'].split('\\')])
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diff_pos = (p2-p1)/(b-a)
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norm = np.linalg.norm(diff_pos)
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print(p1)
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print(p2)
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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()
|
||||
Loading…
Reference in a new issue