pearu / iocbio Goto Github PK

Testing

What steps will reproduce the problem?
1.
doing 'import iocbio.ops' 


What is the expected output? What do you see instead?
causes segmentation fault

What version of the product are you using? On what operating system?
ubuntu 10.10 64bit with epd 2.7.2 64bit (python 2.7.2, numpy 1.6.1 ...)
install iocbio-1.2.2 from source

Please provide any additional information below.
It seems to do with the order of importing the regress_ext extension and the 
numpy/scipy packages. If numpy/scipy are imported first then a segmentation 
fault happens. If the regress_ext is imported first then there is no 
segmentation fault. I got a clue for this from the following link (though I am 
not sure it is the same issue):
http://code.google.com/p/healpy/issues/detail?id=58

To do
1. Time unit uniform, doesn't write minute after number
2. Eventnames into the fourth column not at the end with different units
3. Put different time and rate axises for different channels

Mervi Strath

Exception in runner process:
------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/iocbio/optparse_gui.py", line 153, in __call__
    self.func(*args, **kw)
  File "/usr/local/bin/iocbio.convert", line 117, in runner
    ImageStack(new_images, stack.pathinfo, options=options).save(output_path)
  File "/usr/local/lib/python2.7/dist-packages/iocbio/io/image_stack.py", line 178, in save
    io.save_image_stack(self, path, indices=indices, options=self.options)
  File "/usr/local/lib/python2.7/dist-packages/iocbio/io/io.py", line 447, in save_image_stack
    image_stack.pathinfo.save(pathinfo_txt)
  File "/usr/local/lib/python2.7/dist-packages/iocbio/io/pathinfo.py", line 487, in save
    rotation_angle = self.get_rotation_angle()
  File "/usr/local/lib/python2.7/dist-packages/iocbio/io/pathinfo.py", line 1084, in get_rotation_angle
    self.set_rotation_angle(self.pathinfo.get_rotation_angle())
  File "/usr/local/lib/python2.7/dist-packages/iocbio/io/pathinfo.py", line 426, in set_rotation_angle
    assert isinstance (rotation_angle, (float, int)),`rotation_angle`
AssertionError: None


What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?


Please provide any additional information below.

The attached patch allows to build iocbio on Windows with Microsoft Visual
Studio 2008.

What steps will reproduce the problem?
1. Open image stack captured with iocbio microscope software:
from iocbio.io import load_image_stack  
full_images, full_pathinfo  = load_image_stack('configuration.txt')

2. Get voxel sizes from pathinfo object:
voxel_sizes = full_pathinfo.get_voxel_sizes()

3. Observe that these voxel sizes are in m when the configuration.txt 
clearly specifies that the units are in um.

What is the expected output? What do you see instead?
Units in m, but should retain the original um.

What version of the product are you using? On what operating system?
Latest svn version on ubuntu AMD64.

Please provide any additional information below.
This method should at least specify what the unit of the voxel size is in any 
of a number of ways:
1). Change to get_voxel_size_m
2). Add another method get_voxel_unit
3). Return the unit along with the value in get_voxel_size

Note: set_voxel_size should also support a unit keyword then.