#pydicom_Tkinter.py # # Copyright (c) 2009 Daniel Nanz # This file is released under the pydicom (http://code.google.com/p/pydicom/) # license, see the file license.txt available at # (http://code.google.com/p/pydicom/) # # revision history: # Dec-08-2009: version 0.1 # # 0.1: tested with pydicom version 0.9.3, Python version 2.6.2 (32-bit) # under Windows XP Professional 2002, and Mac OS X 10.5.5, # using numpy 1.3.0 and a small random selection of MRI and # CT images. ''' View DICOM images from pydicom requires numpy: http://numpy.scipy.org/ Usage: ------ >>> import dicom # pydicom >>> import dicom.contrib.pydicom_Tkinter as pydicom_Tkinter # this module >>> df = dicom.read_file(filename) >>> pydicom_Tkinter.show_image(df) ''' from __future__ import with_statement import Tkinter import tempfile import os have_numpy = True try: import numpy as np except: # will not work... have_numpy = False def get_PGM_bytedata_string(arr): '''Given a 2D numpy array as input write gray-value image data in the PGM format into a byte string and return it. arr: single-byte unsigned int numpy array note: Tkinter's PhotoImage object seems to accept only single-byte data ''' if arr.dtype != np.uint8: raise ValueError if len(arr.shape) != 2: raise ValueError # array.shape is (#rows, #cols) tuple; PGM input needs this reversed col_row_string = ' '.join(reversed(map(str, arr.shape))) bytedata_string = '\n'.join(('P5', col_row_string, str(arr.max()), arr.tostring())) return bytedata_string def get_PGM_from_numpy_arr(arr, window_center, window_width, lut_min=0, lut_max=255): '''real-valued numpy input -> PGM-image formatted byte string arr: real-valued numpy array to display as grayscale image window_center, window_width: to define max/min values to be mapped to the lookup-table range. WC/WW scaling is done according to DICOM-3 specifications. lut_min, lut_max: min/max values of (PGM-) grayscale table: do not change ''' if np.isreal(arr).sum() != arr.size: raise ValueError # currently only support 8-bit colors if lut_max != 255: raise ValueError if arr.dtype != np.float64: arr = arr.astype(np.float64) # LUT-specific array scaling # width >= 1 (DICOM standard) window_width = max(1, window_width) wc, ww = np.float64(window_center), np.float64(window_width) lut_range = np.float64(lut_max) - lut_min minval = wc - 0.5 - (ww - 1.0) / 2.0 maxval = wc - 0.5 + (ww - 1.0) / 2.0 min_mask = (minval >= arr) to_scale = (arr > minval) & (arr < maxval) max_mask = (arr >= maxval) if min_mask.any(): arr[min_mask] = lut_min if to_scale.any(): arr[to_scale] = ((arr[to_scale] - (wc - 0.5)) / (ww - 1.0) + 0.5) * lut_range + lut_min if max_mask.any(): arr[max_mask] = lut_max # round to next integer values and convert to unsigned int arr = np.rint(arr).astype(np.uint8) # return PGM byte-data string return get_PGM_bytedata_string(arr) def get_tkinter_photoimage_from_pydicom_image(data): ''' Wrap data.pixel_array in a Tkinter PhotoImage instance, after conversion into a PGM grayscale image. This will fail if the "numpy" module is not installed in the attempt of creating the data.pixel_array. data: object returned from pydicom.read_file() side effect: may leave a temporary .pgm file on disk ''' # get numpy array as representation of image data arr = data.pixel_array.astype(np.float64) # pixel_array seems to be the original, non-rescaled array. # If present, window center and width refer to rescaled array # -> do rescaling if possible. if ('RescaleIntercept' in data) and ('RescaleSlope' in data): intercept = data.RescaleIntercept # single value slope = data.RescaleSlope # arr = slope * arr + intercept # get default window_center and window_width values wc = (arr.max() + arr.min()) / 2.0 ww = arr.max() - arr.min() + 1.0 # overwrite with specific values from data, if available if ('WindowCenter' in data) and ('WindowWidth' in data): wc = data.WindowCenter ww = data.WindowWidth try: wc = wc[0] # can be multiple values except: pass try: ww = ww[0] except: pass # scale array to account for center, width and PGM grayscale range, # and wrap into PGM formatted ((byte-) string pgm = get_PGM_from_numpy_arr(arr, wc, ww) # create a PhotoImage # for as yet unidentified reasons the following fails for certain # window center/width values: # photo_image = Tkinter.PhotoImage(data=pgm, gamma=1.0) # Error with Python 2.6.2 under Windows XP: # (self.tk.call(('image', 'create', imgtype, name,) + options) # _tkinter.TclError: truncated PPM data # OsX: distorted images # while all seems perfectly OK for other values of center/width or when # the PGM is first written to a temporary file and read again # write PGM file into temp dir (os_id, abs_path) = tempfile.mkstemp(suffix='.pgm') with open(abs_path, 'wb') as fd: fd.write(pgm) photo_image = Tkinter.PhotoImage(file=abs_path, gamma=1.0) # close and remove temporary file on disk # os.close is needed under windows for os.remove not to fail try: os.close(os_id) os.remove(abs_path) except: pass # silently leave file on disk in temp-like directory return photo_image def show_image(data, block=True, master=None): ''' Get minimal Tkinter GUI and display a pydicom data.pixel_array data: object returned from pydicom.read_file() block: if True run Tk mainloop() to show the image master: use with block==False and an existing Tk widget as parent widget side effects: may leave a temporary .pgm file on disk ''' frame = Tkinter.Frame(master=master, background='#000') if 'SeriesDescription' in data and 'InstanceNumber' in data: title = ', '.join(('Ser: ' + data.SeriesDescription, 'Img: ' + str(data.InstanceNumber))) else: title = 'pydicom image' frame.master.title(title) photo_image = get_tkinter_photoimage_from_pydicom_image(data) label = Tkinter.Label(frame, image=photo_image, background='#000') # keep a reference to avoid disappearance upon garbage collection label.photo_reference = photo_image label.grid() frame.grid() if block==True: frame.mainloop()