Normally the input files for Labelit must have sequential numbering
like lysozyme_001.cbf. The file name "DX-CORRECTIONS.cbf" causes the
reported error as it does not conform to this format.
Nick
On Fri, Jan 11, 2013 at 9:51 AM, Tim Gruene <[log in to unmask]> wrote:
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> The formatting of icedove probably created confusion, but these error
> message come from running labelit.png WITH the file DX-CORRECTIONS.cbf
> as one and only command line option and no output is created. adxv has
> not problem dealing with XDS cbf-files.
>
> Tim
>
> On 01/11/2013 06:43 PM, Nat Echols wrote:
>> I think the help message refers to another program. Anyway, it's
>> an extremely simple script - having examined the code, the
>> command-line invocation is:
>>
>> labelit.png input_file [output_file]
>>
>> and that's it - no other options available. But Nick or I will fix
>> it so it prints something more useful if run without arguments.
>>
>> -Nat
>>
>> On Fri, Jan 11, 2013 at 9:33 AM, Frank von Delft
>> <[log in to unmask]> wrote:
>>> I got that error blurb too when I run without an image on the
>>> commandline. Not very elegant.
>>>
>>> Try: labelit.png --help
>>>
>>>
>>>
>>>
>>> On 11/01/2013 16:34, Tim Gruene wrote:
>>>>
>> Hi Nat!
>>
>> How recent is recent? From today's 'phenix-online.org': "New Phenix
>> version 1.8.1 now available", but
>>
>> tg@slartibartfast:~/uni/datasets/nk/xds_run3$
>> labelit.png_1.8.1-1168 DX-CORRECTIONS.cbf Traceback (most recent
>> call last): File
>>
>> "/xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py",
>>
>>
> line 27, in <module>
>> OV = overlay_plain(infile,graphics_bin) File
>>
>> "/xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py",
>>
>>
> line 6, in __init__
>> OverlayDriverClass.__init__(self,infile,graphics_bin) File
>>
>> "/xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/overlay_distl.py",
>>
>>
> line 19, in __init__
>> self.I = GenericImageWorker(infile,binning=graphics_bin) File
>> "/xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/graphics/support.py",
>>
>>
> line 12, in __init__
>> images = ImageFiles(imagenames,labelit_commands) File
>>
>> "/xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py",
>>
>>
> line 184, in __init__
>> self.filenames = FileNames(arg_module,phil_params) File
>>
>> "/xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py",
>>
>>
> line 70, in __init__
>> self.interface3_parse_command() File
>>
>> "/xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py",
>>
>>
> line 138, in interface3_parse_command
>>
>> self.interface3_FN_factory(os.path.abspath(file),error_message="File
>>
>>
> name not accepted")
>> File
>>
>> "/xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py",
>>
>>
> line 127, in interface3_FN_factory
>> raise Exception("Input error: "+error_message) Exception: Input
>> error: File name not accepted
>>
>> Compared to: tg@slartibartfast:~/uni/datasets/nk/xds_run3$ adxv
>> -sa DX-CORRECTIONS.cbf DX-CORRECTIONS.tiff Adxv Version 1.9.8
>> Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems
>> Corporation Recognized CBF format data. Warning: Could not find
>> diffrn_frame_data or diffrn_data_frame
>> tg@slartibartfast:~/uni/datasets/nk/xds_run3$ identify
>> DX-CORRECTIONS.tiff DX-CORRECTIONS.tiff TIFF 768x768 768x768+0+0
>> 8-bit PseudoClass 256c 592KB 0.000u 0:00.000
>>
>> Cheers, Tim
>>
>> On 01/10/2013 09:59 PM, Frank von Delft wrote:
>>>>>>
>>>>>> Brilliant - thanks Nat!! Easy to work around that
>>>>>> feature.
>>>>>>
>>>>>> And thanks Nick!!
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------- Original Message -------- Subject: Re:
>>>>>> [ccp4bb] Convert cbf to png/tiff? Date: Thu, 10 Jan
>>>>>> 2013 12:47:21 -0800 From: Nat Echols
>>>>>> <[log in to unmask]> To: Frank von Delft
>>>>>> <[log in to unmask]>
>>
>>
>>
>>
>>
>>
>>>>>>
>>>>>>
>>>>>> Using any recent Phenix distribution:
>>>>>>
>>>>>> labelit.png file_name
>>>>>>
>>>>>> For reasons unknown to me, the output is named "plain.png"
>>>>>> - I will bug Nick about this.
>>>>>>
>>>>>> On Thu, Jan 10, 2013 at 12:36 PM, Frank von Delft
>>>>>> <[log in to unmask]> wrote:
>>>>>>>
>>>>>>> Hello all - anybody know an easy way to convert CBF
>>>>>>> images (Pilatus) into something lossless like tiff or
>>>>>>> png?
>>>>>>>
>>>>>>> Ideally *easy* as in r e a l l y e a s y and not
>>>>>>> requiring extensive installation of dependencies and
>>>>>>> stuff. Because then I might as well write my own stuff
>>>>>>> using cbflib and PIL in python.
>>>>>>>
>>>>>>> Thanks! phx
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>> -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr.
>> 4 D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
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--
Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Physical Biosciences Division
Lawrence Berkeley National Laboratory
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