From P.Nanda at andor.com  Wed Jan 16 01:05:48 2013
From: P.Nanda at andor.com (Pariksheet Nanda)
Date: Wed, 16 Jan 2013 00:05:48 +0000
Subject: [iQ-users] Need extra dimension and timestamps in duplicate dataset,
 but iQImage.duplicate() does not allow creating an extra dimension
Message-ID: <480E81CC9EFEE24B8A13EA161EBD3114AED3D764@CT-EXCH-01.andortech.net>

Hi Patrick,

> Creating "ROIs" over a FRAPPA dataset for presentation purposes, by
> adding a new channel dimension to write the ROI data.  However in
> the new dataset the new dimension should also use the timestamps of
> the original dataset to be useful in the iQ Analysis window.

> 1. Is there a way to copy timestamps of one dataset to another?

> 2. Alternatively is there a way to add another dimension to a
>    duplicated dataset?


You can copy the timestamps from your original single-channel dataset
to your new image this way:

#----------------------------------------------------------------------
from imagedisk import iQImageDisk
from numpy import zeros, concatenate

## Get stamps of the original dataset
##
stamps = [im.getStamp(i) for i in range(im.nframes())]

## Add channel to the original data and save in the new image
##
data = im[:]
# only add 1 channel, keeping other dimensions the smae
extra_channel_shape = list(data.shape)
extra_channel_shape[1] = 1
extra_channel = zeros(extra_channel_shape, dtype=im.dtype)
# FIXME: There's an indexing bug in this concatenate statement, where
# alternate frames have channel data instead of the frame pair.  Fix
# may require numpy fancy indexing to fix or using iQImage.slice2index
data_with_new_channel = concatenate( (data, extra_channel), axis=1)
im2 = id.newImage('extra_channel_image',
                  data_with_new_channel, im.dimNames)

## Write stamps to the new dataset
##
for i in im2.slice2index[:,0]:
    im2.setStamp(i, stamps[i])
#----------------------------------------------------------------------

I'm curious if/how you are able to interleave the channels correctly
`data_with_new_channel` in the above script is not indexed properly.

Perhaps it would be generally useful to hack the iQImage class in
./PythonEngine/Python/imagedisk/__init__.py to have a "merge datasets"
feature, or one could pass an optional "newaxis" argument to
iQImage.duplicate() to create a new dimension at the appropriate
position.  What do you think?

Pariksheet

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