def _convert(self):
print('open data converving start now')
tot_convert_time = 0
for root, dirs, files in os.walk(self.dlserver_path):
for file in files:
if '.dcm' in file:
dcm_path=os.path.join(root, file)
print('dcm path', dcm_path)
dicom_read = dicom.read_file(dcm_path)
try:
if '3D' in dicom_read.SeriesDescription:
x_save_path = dcm_path[:dcm_path.find('/upload')+7] + '/x'
print('x_save_path', x_save_path)
if not os.path.exists(x_save_path):
os.makedirs(x_save_path)
convert_s_time = time.time()
print('save name', x_save_path + '/' + dcm_path[dcm_path.find('/upload')+8:-4] + '.jpg')
mritopng.convert_file(dcm_path, x_save_path + '/' + dcm_path[dcm_path.find('/upload')+8:-4] + '.jpg')
convert_e_time = time.time()
tot_convert_time += convert_e_time - convert_s_time
except AttributeError:
pass
print('converting Finished. Converting time', tot_convert_time)
def test_convert_file_with_negative_values(self):
""" Tests DICOM files with negative values, which are clipped to 0 """
cases = ['000012.dcm', '000017.dcm']
curr_path = os.path.dirname(os.path.realpath(__file__))
for case in cases:
sample_path = os.path.join(curr_path, 'data', 'samples', case)
expected_path = os.path.join(curr_path, 'data', 'expected',
case + '.png')
actual_path = os.path.join(tempfile.gettempdir(),
'%s.%s' % (uuid.uuid4(), "png"))
print('Actual File Path: %s' % actual_path)
# Try the file conversion
try:
mritopng.convert_file(sample_path, actual_path)
except Exception as err:
self.fail('%s' % err)
self.assertTrue(
filecmp.cmp(actual_path, expected_path),
'PNG generated from dicom1 does not match the expected version'
)
def dicom_to_png(self):
# get dicom file list
dcm_file_list = [
file for file in os.listdir(self.input_path)
if file.endswith(".dcm")
]
dcm_file_list.sort()
parent_path = self.input_path + "/../"
png_dir_name = self.get_dir_name(self.input_path) + "toPng"
# make new png dir with png name
png_dir_path = os.path.join(parent_path, png_dir_name)
utils.maybe_mkdir(png_dir_path)
for dcm in dcm_file_list:
dcm_name = dcm[:-4]
png_name = dcm_name + ".png"
# convert one dicom file to one png file
mritopng.convert_file(os.path.join(self.input_path, dcm),
os.path.join(png_dir_path, png_name),
auto_contrast=True)
print("Successfully process dicom to png your new file created at {}".
format(png_dir_path))
return
def cleanedPhosphorusData():
default_png = os.path.join(APP_ROOT, 'uploads', 'converted',
'Default_MRI.png')
upload_png = os.path.join(APP_ROOT, 'uploads', 'converted',
'Upload_MRI.png')
upload_dcm = os.path.join(APP_ROOT, 'uploads', 'mri', 'Upload_MRI.dcm')
return_image = default_png
encoded_string = "Error while image encoding"
# Check whether the upload MRI file exist
try:
if os.path.isfile(upload_dcm):
if os.path.isfile(upload_png):
os.remove(upload_png)
try:
# Convert the MRI file to PNG file
mritopng.convert_file(upload_dcm, upload_png)
return_image = upload_png
except Exception as exp:
app.logger.error(str(exp))
elif os.path.isfile(upload_png):
return_image = upload_png
# Convert the image
with open(return_image, "rb") as image:
encoded_string = base64.b64encode(image.read())
except Exception as exception:
app.logger.error(str(exception))
#return send_file(return_image, mimetype='image/png')
return encoded_string
def test_convert_file_auto_contrast(self):
cases = ['dicom1', '000012.dcm', '000017.dcm']
curr_path = os.path.dirname(os.path.realpath(__file__))
os.makedirs(os.path.join(test_out_path, 'auto-contrast'))
for case in cases:
sample_path = os.path.join(curr_path, 'data', 'samples', case)
expected_path = os.path.join(curr_path, 'data', 'expected',
'auto-contrast', case + '.png')
actual_path = os.path.join(test_out_path, 'auto-contrast',
case + '.png')
print('Actual File Path: %s' % actual_path)
# Try the file conversion
try:
print('>>> Here')
mritopng.convert_file(sample_path,
actual_path,
auto_contrast=True)
print('<<<')
except Exception as err:
traceback.print_exc(file=sys.stdout)
self.fail('%s' % err)
self.assertTrue(
filecmp.cmp(actual_path, expected_path),
'PNG generated from dicom1 does not match the expected version'
)
def convertImg(dicomImage):
print("Image: " + dicomImage)
outputImg = dicomImage.split('.')
mritopng.convert_file(os.path.join(folder_path, dicomImage),
os.path.join(folder_path, outputImg[0] + '.jpg'),
auto_contrast=True)
convertedImg = os.path.join(folder_path, outputImg[0] + '.jpg')
return convertedImg
def convert_dcm_to_png(root_dir, source_dir):
if not os.path.exists(os.path.join(root_dir, 'png')):
os.makedirs(os.path.join(root_dir, 'png'))
dcm_data_path = glob(os.path.join(root_dir, source_dir, '*.dcm'))
for idx in range(np.shape(dcm_data_path)[0]):
complit_data_name = re.split('/|[.]|\\\\', dcm_data_path[idx])[-2]
data_name = re.split('/|[_]', complit_data_name)[0]
print(os.path.join(root_dir, source_dir, complit_data_name, '.dcm'))
mritopng.convert_file(dcm_data_path[idx],os.path.join(root_dir, 'png', data_name + '.png'))
def test_convert_file(self):
""" Tests conversion of a single DICOM file """
curr_path = os.path.dirname(os.path.realpath(__file__))
sample_path = os.path.join(curr_path, 'data', 'samples', 'dicom1')
expected_path = os.path.join(curr_path, 'data', 'expected', 'dicom1.png')
actual_path = os.path.join(test_out_path, 'dicom1.png')
print('Actual File Path: %s' % actual_path)
# Try the file conversion
try:
mritopng.convert_file(sample_path, actual_path)
except Exception as err:
self.fail('%s' % err)
self.assertTrue(filecmp.cmp(actual_path, expected_path),
'PNG generated from dicom1 does not match the expected version')
def post(self, request):
serializer = DicomSerializer(data=request.data)
filename = str(request.data['dicom'])
folder_path = os.path.join(settings.BASE_DIR, 'static_files')
dicom_path = folder_path + '/dicom/' + filename
if '.dcm' in filename:
filename = change_extension.splitext(filename)[0]
png_path = folder_path + '/dicom/png/' + filename + '.png'
# print(png_path)
if serializer.is_valid():
serializer.save()
# dicom_path = folder_path+str(serializer.data['dicom'])
makedirs(folder_path + '/dicom/png/', exist_ok=True)
mritopng.convert_file(dicom_path, png_path)
png_path = '/media/dicom/png/' + filename + '.png'
return Response({"path": png_path}, status=201)
return Response(serializer.errors, status=400)
RefDs.pixel_array.dtype # In[6]: lstFilesDCM[26][:-4] # In[7]: # png 파일로 저장 mritopng.convert_file(lstFilesDCM[26], lstFilesDCM[26][:-4]+".png") # In[8]: src = cv.imread(lstFilesDCM[26][:-4]+".png",-1) # In[9]: type(src) src.dtype
# files = glob.glob("*.dcm")
# for file in tqdm(files[:1]):
# try:
# fname = file[:-4] + ".png"
#
# data = pydicom.dcmread(file)
# img = data.pixel_array
# print(img.shape)
# plt.imsave(os.path.join(test_result_path, fname), img, cmap=plt.cm.bone)
# # Image.save(os.path.join(test_result_path, fname))
# # cv2.imwrite(os.path.join(test_result_path, fname), img)
# except:
# print(f"unexpected error occur: {file}")
print("Converting Test Datasets ... ")
os.chdir(val_dicom_path)
files = glob.glob("*.dcm")
for file in tqdm(files):
try:
fname = file[:-4] + ".png"
mritopng.convert_file(os.path.join(val_dicom_path, file),
os.path.join(val_result_path, fname))
# data = pydicom.dcmread(file)
# img = data.pixel_array
# print(img.shape)
# plt.imsave(os.path.join(test_result_path, fname), img, cmap=plt.cm.bone)
# Image.save(os.path.join(test_result_path, fname))
# cv2.imwrite(os.path.join(test_result_path, fname), img)
except:
print(f"unexpected error occur: {file}")