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--- documents:110816pyip_cooking [2011/09/22 21:47] – 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]]>
@@ Line 106: / Line 106: @@
 ==== 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 mayavi2.
+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]].
-<sxh python>
+<code python linenums:1>
 from matplotlib import mlab as matp
 filename = '/Users/miura/data.txt'
@@ Line 123: / Line 123: @@
     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()
-</sxh>
+</code>
 [{{ :documents:figure20110923:mayaviexample.png?250| plotting data with mayavi}}]
@@ Line 138: / Line 138: @@
 ipython -wthread
 </code>
-or incase of newer ipython
+or incase of newer ipython (version >= 1.1)
 <code>
 ipython --i
@@ Line 160: / Line 160: @@
 Note that in this example,
-<sxh python>
+<code python>
 from mayavi import mlab as maya
-</sxh>
+</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}}]