Problem with isContinuous 'PhiWidth'

[KyleStiers]

Hello

When I attempt to run xdsme providing the set of diffraction images I get the following error:

Warning: time data 'Thu Aug 23 2018 14:33:01.647976' does not match format '%a %b %d %H:%M:%S %Y'
... Using time.time() instead.
Traceback (most recent call last):
  File "/programs/x86_64-linux/xdsme/20170725/bin/noarch/xdsme", line 1739, in <module>
    if not _coll.isContinuous(inputf):
  File "/data/programs/x86_64-linux/xdsme/20170725/XDS/XIO/XIO.py", line 861, in isContinuous
    phi_range = self.image.header['PhiWidth']
KeyError: 'PhiWidth'

Is this related to Issue #1 ?

Any ideas on a workaround or fix?

[JunAishima]

could you describe what type of images you're using? I've used ADSC and Eiger HDF5 files without any problems. the directory XIO/plugins has some interpreters (*_interpreter.py) that should give you an idea of what header values need to be populated for PhiWidth to get a value.

[KyleStiers]

I'm using images from a Pilatus detector. I ran xio_info on one of the images and got this:

Warning: time data 'Thu Aug 23 2018 14:33:01.647976' does not match format '%a %b %d %H:%M:%S %Y'
... Using time.time() instead.
>> Interpreting header of image:  /data/------/082318/10-01/10-01_1/10-01_1_0001.img
>> Image format:      adsc
{'BeamX': 147.2471,
 'BeamY': 142.0419,
 'DateSeconds': 1538589618.656785,
 'DateStr': 'Thu Aug 23 2018 14:33:01.647976',
 'Distance': 180.0,
 'EdgeResolution': 1.4840371378948147,
 'EndianType': '<',
 'ExposureTime': 0.2,
 'HeaderSize': 3072,
 'Height': 2820,
 'ImageType': 'adsc',
 'Message': [''],
 'PixelX': 0.1001,
 'PixelY': 0.1001,
 'SensorThickness': 0.0,
 'TwoTheta': 0.0,
 'Wavelength': 1.000032,
 'Width': 2952}
>> Loading /data/------/082318/10-01/10-01_1/10-01_1_0001.img
>> 2952 x 2820 pixels
>> Distance: 180.0 mm, Lambda: 1.000 A
Traceback (most recent call last):
  File "/programs/x86_64-linux/xdsme/20170725/bin/noarch/xio_info", line 69, in <module>
    _test1(filename)
  File "/programs/x86_64-linux/xdsme/20170725/bin/noarch/xio_info", line 32, in _test1
    im.data_info()
  File "/data/programs/x86_64-linux/xdsme/20170725/XIO/XIO.py", line 458, in data_info
    data = self.getData()
  File "/data/programs/x86_64-linux/xdsme/20170725/XIO/XIO.py", line 493, in getData
    _data = struct.unpack(_fmt, _data)
struct.error: unpack requires a string argument of length 17428608

So it is an ADSC type, apparently, but still not working. Can I supply PhiWidth from the command-line somehow to make sure it's getting the right value?

[JunAishima]

I don't think it should be getting ADSC as the type - XIO.py should be recognizing the header as either a "minicbf" or "MSC Pilatus" which look like the two Pilatus types that can be recognized.

Can you show the miniCBF header, if it is a CBF file? or is it a tiff? tiff may be a problem because the two types above seem to assume a miniCBF file coming out of the Pilatus.

[legrandp]

From the pixel size, Height and Width, this can't be a Pilatus image. Could you send us an image so that we can check ?

[JunAishima]

this looks like it's from ALS beamline 4.2.2 in Berkeley, CA, USA (just googled the image dimensions). this is not a large production common detector so there will not be any code that can read the images in xdsme yet. it's a fast CMOS detector capable of shutterless operation

[KyleStiers]

Woops, you're right - I was thinking of our home source but these images are from ALS 4.2.2 with a CMOS-based Taurus-1 detector. So I guess that explains it

[KyleStiers]

I guess the question I have left then is why XDS processing works on these images directly, but not in xdsme. Is the problem just with gathering the necessary metadata on the file-type?

[legrandp]

Yes. XDS is almost not reading the header's metadata. That's where xdsme helps using the XIO module. Since, data from this particular detector are not frequent, I have never had a request to make xdsme compatible with it. I may be not so difficult.

[KyleStiers]

Thanks for looking into it!