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# Copyright (c) 2009 Daniel Nanz
# This file is released under the pydicom
# (
# license, see the file LICENSE available at
# (
# 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:
>>> import pydicom # pydicom
>>> import pydicom.contrib.pydicom_Tkinter as pydicom_Tkinter # this module
>>> df = pydicom.read_file(filename)
>>> pydicom_Tkinter.show_image(df)
import tempfile
import os
from pydicom.compat import in_py2
if in_py2:
import Tkinter as tkinter
have_numpy = True
import numpy as np
except ImportError:
# 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([str(x) for x in arr.shape]))
bytedata_string = '\n'.join(('P5', col_row_string, str(arr.max()),
return bytedata_string
def get_PGM_from_numpy_arr(arr,
'''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
wc = wc[0] # can be multiple values
except Exception:
ww = ww[0]
except Exception:
# 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:
# ('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:
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
except Exception:
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)))
title = 'pydicom image'
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
if block:
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