def overlay_test(self):
# filename =
# r'c:\Data\kky\pro mechaniku 21.12.2012\53009707\Export0000\SR0000'
# filename = r'c:\Data\kky\pro mechaniku
# 21.12.2012\52496602\Export0001\SR0000'
# filename = r'c:\Data\kky\pro mechaniku
# 21.12.2012\54559730\Export0000\SR0000'
filename = r'c:\Data\kky\pro mechaniku 21.12.2012\53596059\Export0000\SR0000' # noqa
# dcr = dcmreaddata.DicomReader(
# r'c:\Data\kky\pro mechaniku 21.12.2012\52496602\Export0001\SR0000')
dcr = dcmreaddata.DicomReader(filename)
data3d = dcr.get_3Ddata()
overlay = dcr.get_overlay()
win_w = 350
win_c = 50
min_w = win_c - (win_w / 2.)
max_w = win_c + (win_w / 2.)
for key in overlay.keys():
overlay = overlay[key]
for i in range(overlay.shape[0]):
plt.figure(), plt.gray()
plt.subplot(121), plt.imshow(data3d[i, :, :],
vmin=min_w,
vmax=max_w)
plt.subplot(122), plt.imshow(overlay[i, :, :])
cv2.imwrite(filename + '/overlay_%i.png' % i, data3d[i, :, :])
plt.show()
def loadDcmDir(self):
self.statusBar().showMessage('Reading DICOM directory...')
QApplication.processEvents()
if self.dcmdir is None:
self.dcmdir = dcmreader.get_dcmdir_qt(app=True)
if self.dcmdir is not None:
dcr = dcmreader.DicomReader(os.path.abspath(self.dcmdir),
qt_app=self)
else:
self.statusBar().showMessage('No DICOM directory specified!')
return
if dcr.validData():
self.dcm_3Ddata = dcr.get_3Ddata()
self.dcm_metadata = dcr.get_metaData()
self.voxel_sizemm = np.array(self.dcm_metadata['voxelsizemm'])
self.setVoxelVolume(self.voxel_sizemm)
self.setLabelText(self.text_dcm_dir, self.dcmdir)
self.setLabelText(self.text_dcm_data, self.getDcmInfo())
self.statusBar().showMessage('Ready')
self.setLabelText(self.text_seg_in, 'DICOM reader')
else:
self.statusBar().showMessage('No DICOM data in direcotry!')
def loadDcmDir(self, event=None, filename=None):
self.statusBar().showMessage('Loading DICOM data...')
QApplication.processEvents()
# TODO uninteractive Serie selection
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(datadir)
datadir = dcmr.get_dcmdir_qt(self.qt_app)
# @TODO dialog v qt
reader = dcmr.DicomReader(datadir) #, qt_app=self.qt_app)
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
self.inps['series_number'] = reader.series_number
self.inps['datadir'] = datadir
self.statusBar().showMessage('DICOM data loaded')
def __ReadFromDirectory(self, datapath, start, stop, step):
if dcmr.is_dicom_dir(datapath): # reading dicom
logger.debug('Dir - DICOM')
reader = dcmr.DicomReader(datapath, qt_app=None, gui=True)
data3d = reader.get_3Ddata(start, stop, step)
metadata = reader.get_metaData()
metadata['series_number'] = reader.series_number
metadata['datadir'] = datapath
self.overlay_fcn = reader.get_overlay
else: # reading image sequence
import SimpleITK as sitk
logger.debug('Dir - Image sequence')
logger.debug('Getting list of readable files...')
flist = []
for f in os.listdir(datapath):
try:
sitk.ReadImage(os.path.join(datapath, f))
except:
logger.warning("Cant load file: " + str(f))
continue
flist.append(os.path.join(datapath, f))
flist.sort()
logger.debug('Reading image data...')
image = sitk.ReadImage(flist)
logger.debug('Getting numpy array from image data...')
data3d = sitk.GetArrayFromImage(image)
metadata = {} # reader.get_metaData()
metadata['series_number'] = 0 # reader.series_number
metadata['datadir'] = datapath
spacing = image.GetSpacing()
metadata['voxelsize_mm'] = [
spacing[2],
spacing[0],
spacing[1],
]
return data3d, metadata
def import_dir(self, datadir):
reader = dcmr.DicomReader(datadir)
self.data3d = reader.get_3Ddata()
self.metadata = reader.get_metaData()
#self.data3d, self.metadata = dcmr.dcm_read_from_dir(datadir)
self.voxelsize_mm = np.array(self.metadata['voxelsize_mm'])