Hallo!
To read uncompressed TIFF files I use the freeimage plugin. The reading
works great but since last week I need to save a summed Image. I used the
io.imsave() with the freeimage plugin but by default it writs a compressed
TIFF file. The freeimage documentation provides Flags to use for different
compressions or for a non compressed type (TIFF_NONE). Can someone tell me
how to pass theses Flags to the plugin?
I saw that Christophs 'tifffile' plugin does the job but still I would like
to know how to use the freeimage plug-n for it.

Thanks!

Siggi

This functionality is not exposed by the imsave() apparatus, but can be accessed by the image writing functions in the plugin that imsave() calls.

A quick scan through the source code is likely to be the most helpful thing, regarding the available flags, etc:
https://github.com/scikits-image/scikits-image/blob/master/skimage/io...

In particular, the freeimage_plugin.write() function, around which freeimage_plugin.imsave() is a thin wrapper, allows you to set various flags.
So:
import skimage.io._plugins.freeimage_plugin as fi
image = fi.read('/path/to/whatever')
fi.write(image, 'whatever.tif', fi.IO_FLAGS.TIFF_NONE)

Zach

On May 12, 2012, at 4:04 AM, Sigmund wrote:

Thanks! Works great!

Siggi

Hallo!

As I wrote, the workaround:

Am Samstag, 12. Mai 2012 15:47:10 UTC+2 schrieb Zachary Pincus:

Traceback (most recent call last):
  File "G:\Marwen\Summer.py", line 67, in <module>
    fi.write(summation,
str(datensatz)+"_interval-"+str(interval_length)+"_"+str(count)+'.tif',
fi.IO_FLAGS.TIFF_NONE)
  File
"C:\Python27\lib\site-packages\skimage\io\_plugins\freeimage_plugin.py",
line 538, in write
    bitmap, fi_type = _array_to_bitmap(array)
  File
"C:\Python27\lib\site-packages\skimage\io\_plugins\freeimage_plugin.py",
line 604, in _array_to_bitmap
    raise ValueError('Cannot write arrays of given type and shape.')
ValueError: Cannot write arrays of given type and shape.

I checked the .dtype of the array and compared them to the one on the 32bit
and the OS X system but coutn't see any difference.

I'm reading several Images with
numpy.array(io.imread(bild, plugin="freeimage"),dtype=np.int32)
and sum then up one by one to write them out afterwards as one file.

Siggi

This may be an issue with the underlying FreeImage library, or a lingering 64-bit bug in the wrappers. So if you could do a bit more sleuthing and figure out the exact trigger for the problem, that would be very helpful in fixing it.

Thanks,
Zach

On Jul 9, 2012, at 9:13 AM, Sigmund wrote:

same problem with io.imsave

Traceback (most recent call last):
  File "G:\Marwen\Summer.py", line 61, in <module>
io.imsave("test.tif",summation, plugin="freeimage")
  File "C:\Python27\lib\site-packages\skimage\io\_io.py", line 129, in
imsave return call_plugin('imsave', fname, arr, plugin=plugin,
**plugin_args)
  File "C:\Python27\lib\site-packages\skimage\io\_plugins\plugin.py", line
88, in call return func(*args, **kwargs)
  File
"C:\Python27\lib\site-packages\skimage\io\_plugins\freeimage_plugin.py",
line 668, in imsave write(img, filename)
  File
"C:\Python27\lib\site-packages\skimage\io\_plugins\freeimage_plugin.py",
line 538, in write bitmap, fi_type = _array_to_bitmap(array)
  File
"C:\Python27\lib\site-packages\skimage\io\_plugins\freeimage_plugin.py",
line 604, in _array_to_bitmap raise ValueError('Cannot write arrays of
given type and shape.')
ValueError: Cannot write arrays of given type and shape.

siggi

without the try: and raise ValueError in the freeimage_plugin.py it returns:

Traceback (most recent call last):
  File "G:\Marwen\Summer.py", line 61, in
<module>io.imsave("test.tif",summation, plugin="freeimage")
  File "C:\Python27\lib\site-packages\skimage\io\_io.py", line 129, in
imsave return call_plugin('imsave', fname, arr, plugin=plugin,
**plugin_args)
  File "C:\Python27\lib\site-packages\skimage\io\_plugins\plugin.py", line
88, in call return func(*args, **kwargs)
  File
"C:\Python27\lib\site-packages\skimage\io\_plugins\freeimage_plugin.py",
line 669, in imsave write(img, filename)
  File
"C:\Python27\lib\site-packages\skimage\io\_plugins\freeimage_plugin.py",
line 538, in write bitmap, fi_type = _array_to_bitmap(array)
  File
"C:\Python27\lib\site-packages\skimage\io\_plugins\freeimage_plugin.py",
line 601, in _array_to_bitmap fi_type = FI_TYPES.fi_types[(dtype.type,
n_channels)]
KeyError: (<type 'numpy.int32'>, 1)

I'm afraid that is all I can do with my limited skills...

I proved myselfe wrong ;-)

It is working if I chose numpy.float32 as dtype!

uint32 doesn't work either. Leads to KeyError: (<type 'numpy.int64'>, 1)

Siggi

Zach

Hey!

Whil writing the test code I found out that saving the array by itself
doesn't cause the error. Only after summing two arrays it fails.

import numpy as np
import skimage.io as io
io.use_plugin("freeimage", "imread")
one = np.ones([2048,2048],dtype=np.int32)
two = np.zeros([2048,2048],dtype=np.int32)
summation = one + two
io.imsave("test.tif",summation, plugin="freeimage")

 not using the freeimage plugin in not failing.

Siggi

On Jul 10, 2012, at 9:35 AM, Sigmund wrote:

In summary.
It is working on :
Python 2.7.1 |EPD 7.0-2 (32-bit)| Win 7 32
Python 2.7.2 |EPD 7.2-2 (64-bit)| Mac OSX
And not working on:
Python 2.7.3 |EPD 7.3-1 (64-bit)| Win 7 64
Python 2.7.2 IEPD 7.2-2 (32-bit)| Win XP

Hopefully someone can try to verify this. Strange, too, that it would fail on XP but work on Win 7 32-bit. Perhaps that's a red herring and it has to do with the EPD version?

On Jul 12, 2012, at 8:41 AM, Sigmund wrote:

import numpy as np
one = np.ones([2048,2048],dtype=np.int32)
two = np.zeros([2048,2048],dtype=np.int32)
summation = one + two

assert repr(summation.dtype) == repr(one.dtype)
assert summation.dtype == one.dtype
assert hash(summation.dtype) == hash(one.dtype)

assert repr(summation.dtype.type) == repr(one.dtype.type)
assert summation.dtype.type != one.dtype.type
assert hash(summation.dtype.type) != hash(one.dtype.type)

I submitted a PR at
<https://github.com/scikits-image/scikits-image/pull/214>

Christoph

On 7/12/2012 7:09 AM, Zachary Pincus wrote: