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--- documents:110816pyip_cooking [2011/08/16 23:39] – created kota
+++ documents:110816pyip_cooking [2016/05/25 07:56] (current) – [plot 3D coordinates using Mayavi] kota
@@ Line 9: / Line 9: @@
 === Tiff file to numpy.ndarray ===
-<sxh python>
+<code python>
 >>> import cv
 >>> img = cv.imread('/Users/miura/img/blobs.tif')
 >>> type(img)
 >>> <type 'numpy.ndarray'>
-</sxh>
+</code>
   * cv.imread reads only the first frame in tiff stack.
@@ Line 21: / Line 21: @@
 === Tiff file to Iplimage ===
-<sxh python>
+<code python>
 In [40]: img = cv.LoadImage('/Users/miura/img/blobs.tif')
 In [41]: img
 Out[41]: <iplimage(nChannels=3 width=256 height=254 widthStep=768 )>
-</sxh>
+</code>
@@ Line 35: / Line 35: @@
 === Tiff to numpy.ndarray, Single Image ===
-<sxh python>
+<code python>
 In [44]: import tifffile as tff
 In [50]: tiffimg = tff.TIFFfile('/Users/miura/img/blobs.tif')
@@ Line 43: / Line 43: @@
 In [53]: type(img)
 Out[53]: <type 'numpy.ndarray'>
-</sxh>
+</code>
 === Tiff to numpy.ndarray, Stack Image ===
-<sxh python>
+<code python>
 In [54]: tiffimg = tff.TIFFfile('/Users/miura/img/flybrainG.tif')
 In [55]: img = tiffimg.asarray()
@@ Line 57: / Line 57: @@
 In [62]: type(img10)
 Out[62]: <type 'numpy.ndarray'>
-</sxh>
+</code>
   * if the image file is a single frame image, not so different from the others
   * Stack tiff file is loaded peroperly. Single frame is extractable by indexing. In above case, 11th frame is extracted.
@@ Line 67: / Line 67: @@
   * tested with python2.6, openCV 2.2, numpy 1.6.1, OSX10.6.8
-<sxh python>
+<code python>
 >>> import cv
 >>> import numpy as np
@@ Line 78: / Line 78: @@
        [ 7.,  7.,  7.,  7.,  7.]], dtype=float32)
-</sxh>
+</code>
 <[[http://stackoverflow.com/questions/5762440/how-to-transform-a-opencv-cvmat-back-to-ndarray-in-numpy|link]]>
@@ Line 85: / Line 85: @@
   * tested with python2.6, openCV 2.2, numpy 1.6.1, OSX10.6.8
-<sxh python>
+<code python>
 >>> im = cv.CreateImage( ( 5 , 5 ) , 8 , 1 )
 >>> cv.Set( im , 100 )
@@ Line 99: / Line 99: @@
        [100, 100, 100, 100, 100]], dtype=uint8)
-</sxh>
+</code>
 <[[http://stackoverflow.com/questions/5762440/how-to-transform-a-opencv-cvmat-back-to-ndarray-in-numpy|link]]>
+===== Data Visualization =====
+==== plot 3D coordinates using Mayavi ====
+An example script for loading (x, y, y) coordinates data from tab-delimited text file and plot them in 3D using [[http://github.enthought.com/mayavi/mayavi/|mayavi2]].
+<code python linenums:1>
+from matplotlib import mlab as matp
+filename = '/Users/miura/data.txt'
+x1, y1, z1, x2, y2, z2 = matp.load(filename, usecols=[0, 1, 2, 3, 4, 5], unpack=True)
+from mayavi.mlab import points3d
+from mayavi.mlab import plot3d
+from mayavi import mlab as maya
+p1s = points3d(x1, y1, z1, scale_factor=.25, color=(0, 1, 1))
+p2s = points3d(x2, y2, z2, scale_factor=.25, color=(1, 0, 0))
+for idx, xval in enumerate(x1):
+    plin1 = plot3d([x1[idx], x2[idx]], [y1[idx], y2[idx]], [z1[idx], z2[idx]], tube_radius=0.1, colormap='Spectral', color=(0, 0, 1))
+maya.show()
+</code>
+[{{ :documents:figure20110923:mayaviexample.png?250| plotting data with mayavi}}]
+In this example, we assume the follwoing data structure in the file: a pair of coordinates per line, so 6 numbers are in one line separated by tab. It should look like
+<code>
+.0 3.6 4.8 5.1 6.12 7.14
+...
+</code>
+To run this script, the best is to run it from ipython with thread so first you start ipython by
+<code>
+ipython -wthread
+</code>
+or incase of newer ipython (version >= 1.1)
+<code>
+ipython --i
+</code>
+then in the ipython interface,
+<code>
+run exampleMayavi.py
+</code>
+A new window pops up, and after drawing of the scene is finished, you could control the scene by such as
+<code>
+maya.view(100, 40)
+</code>
+or to animate the scene
+<code>
+for i in range (1, 360, 3): maya.view(i, i)
+</code>
+to close the scene,
+<code>
+maya.close()
+</code>
+Note that in this example,
+<code python>
+from mayavi import mlab as maya
+</code>
+since the namespace "mlab" overlaps with matplotlib.mlab.
+==== plot 3D trajectory using Mayavi ====
+To evaluate 3D particle tracking results, trajectories could be plotted by color coding the time.
+[{{ :documents:figure20111219:snapshot3.png?300| Plotting 3D trajectory. Trajectories are colored so that the beginning of frame is blue and gradually become red towards the end of the sequence}}]