Updated Python example

The Python example now features reading and displaying an example DMP
file.
The example.DMP file will be added to the repository once I get the
clearance from the original user.
Additionally we load a "random" image from the web and save that as DMP
to show how to save images as DMP.
Also renamed script :)

Python/DMPFile.py

@@ -1,44 +0,0 @@
-import numpy as np
-
-def readDMPFile(fileName):
-    '''
-    Opens and reads DMP file. Returns numpy ndarray.
-    '''
-    
-    fd = open(fileName, 'rb')
-    
-    #datatype is unsigned short
-    datatype = 'h'
-    numberOfHeaderValues = 3
-    
-    headerData = np.fromfile(fd, datatype, numberOfHeaderValues)
-    
-    imageShape = (headerData[1], headerData[0])
-    
-    imageData = np.fromfile(fd, np.float32, -1)
-    imageData = imageData.reshape(imageShape)
-    
-    return imageData
-
-def writeDMPFile(fileName, np_array):
-    '''
-    Writes numpy ndarray to DMP file.
-    ndArray.dtype should be np.float32. If it not, it will be converted before saving.
-    '''
-    
-    # opens file for writing (binary)
-    fd = open(fileName, 'wb')
-    
-    # create header - must be dtype np.uint16 !!! 
-    width = np.array(np_array.shape[1])
-    height = np.array(np_array.shape[0])
-    
-    header = np.array([width, height, 0], np.uint16)
-    header.tofile(fd)
-    
-    # img data/numpy ndarray
-    # dtype has to be np.float32
-    if np_array.dtype != 'float32':
-        np_array = np_array.astype(np.float32)
-        
-    np_array.tofile(fd)

Python/HandleDMPFiles.py

@@ -0,0 +1,74 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+Python script to read DMP file.
+Written by David Haberthür <david.haberthuer@psi.ch> based on an initial
+version by Martin Nyvlt <martin.nyvlt@gmail.com>
+"""
+
+import numpy
+import os
+import matplotlib.pyplot as plt
+import urllib2
+
+
+def readDMP(filename):
+    """
+    Opens and reads DMP file.
+    Returns a numpy ndarray which can be displayed/written/handled further.
+    """
+    # Open the file
+    dmpfile = open(filename, 'rb')
+    # The DMP file format is a very simple file format; the header consists of
+    # 3 unsigned 16bit integers specifying the image dimensions, followed by a
+    # stream of 32-bit floats in little-endian byte order.
+    # Load Header.  It's first two values are the image size.
+    header = numpy.fromfile(dmpfile, numpy.int16, 3)
+    imageSize = (header[1], header[0])
+    # Load file and reshape to the size from the header
+    image = numpy.fromfile(dmpfile, numpy.float32)
+    image = image.reshape(imageSize)
+    dmpfile.close()
+    return image
+
+
+def writeDMP(array, outputfilename):
+    """
+    Writes numpy ndarray to DMP file.
+    The array.dtype should be numpy.float32.
+    If it's not, it will be converted before saving.
+    """
+    # Open the file for writing (binary)
+    dmpfile = open(outputfilename, 'wb')
+    # Create header. *Must* be dtype numpy.uint16!
+    width = numpy.array(array.shape[1])
+    height = numpy.array(array.shape[0])
+    header = numpy.array([width, height, 0], numpy.uint16)
+    header.tofile(dmpfile)
+    # Write Image data. dtype has to be np.float32
+    if array.dtype != 'float32':
+        array = array.astype(numpy.float32)
+    array.tofile(dmpfile)
+    dmpfile.close()
+
+# Read example DMP file with the function defined above
+DMPFileName = os.path.join(os.getcwd(), '..', 'example.DMP')
+DMP = readDMP(DMPFileName)
+# Show example image
+plt.subplot(121)
+plt.imshow(DMP, cmap='gray')
+plt.title('example.DMP')
+
+# Load some image from the internet and save its green channel as DMP.
+URL = urllib2.urlopen('http://www.psi.ch/sls/tomcat/HomeEN/tomcat_banner.png')
+image = plt.imread(URL)[:, :, 1]
+writeDMP(image, 'randomimage.DMP')
+# Read the image again as DMP and display it
+plt.subplot(122)
+plt.imshow(readDMP('randomimage.DMP'), cmap='gray')
+plt.title('Some random image')
+
+plt.show()
+
+print 'Now open randomimage.DMP in Fiji!'