iQ IDE plugin to export image stamps with sorting

timestamp.py

#BACKGROUND
'''
Saves image stamps, sorted by time, in CSV file on desktop.

FIXME: For this to work, upstream needs to patch imagedisk/__init__.py to use
new 3.x Python style class foo(object): instead of class foo: syntax.
'''

import imagedisk
import iqtools
from numpy import dtype, array, savetxt
from os import path, getenv

FILE_SAVE_FOLDER = 'Desktop'


class iQImage2(imagedisk.iQImage):
    '''
    Monkey patch iQImage with 'metadata' ndarray.
    '''
    _STAMP_DTYPE_DEFAULT = 'float64'
    _STAMP_DTYPE_OVERRIDES = { 'Z': 'float64' }

    def __init__(self, iQImageDisk, title):
        super(iQImage2, self).__init__(iQImageDisk, title)

    @property
    def stamps(self):
        '''
        Structured ndarray of image stamp metadata
        
        >>> im.stamps.dtype.names
        ('Slice', 'Wavelength', 'Time', 'Event')
        >>> im.stamps['Time']
        array([    0,  1998, 14000, 16001, 18001,  ... 12096], dtype=uint64)
        '''
        header = ['Slice'] + im.getStamp(1, showNames=True)[1]

        # Create structured array type.
        dim_type = [self._STAMP_DTYPE_DEFAULT] * len(header)
        if self._STAMP_DTYPE_OVERRIDES != {}:
            for i in range(len(header)):
                if self._STAMP_DTYPE_OVERRIDES.has_key(dim_type[i]):
                    dim_type[i] = self._STAMP_DTYPE_OVERRIDES[dim_type[i]]
        im_metadata_type = dtype(zip(header, dim_type))

        # Construct metadata ndarray.
        array_content = [tuple([n] + im.getStamp(n)) for n in range(im.nslices)]
        metadata_array = array(array_content,
                               dtype=im_metadata_type)
        return metadata_array

imagedisk.iQImage = iQImage2


# Main program.
id = imagedisk.iQImageDisk()
im = iqtools.dialogs.getDataset(id)
if im == None:
    raise RuntimeError, 'User cancelled dataset selection'

# Create and sort the array
metadata = im.stamps
metadata.sort(order=['Time'])

# Write array to file.
file = path.join(
    path.join(getenv('USERPROFILE'), FILE_SAVE_FOLDER),
    '{basename}.{ext}'.format(basename=im.title, ext='txt')
    )
delimiter = ','
header_list =['{0:>11}'.format(dim) for dim in metadata.dtype.names]
header = delimiter.join(header_list) + '\n'
with open(file, 'w') as f:
    f.write(header)
    savetxt(f, metadata, fmt='%11d', delimiter=delimiter)

'''
ChangeLog
=========
2013-09-10  Pariksheet Nanda  <p.nanda@andor.com>

    * stamps: Fixed bug of negative 'Z' values incorrectly being typecast
    to unsigned integers, by introducing new variable DTYPE_OVERRIDES to
    respect values specified in _mm.py of imagedisk module.
    
    * stamps: now a variable instead of a function.

2012-05-27  Pariksheet Nanda  <p.nanda@andor.com>

    * Initial release.
'''