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 <[email protected]> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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 >> <[email protected]> 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 >>>>>> <[email protected]> To: Frank von Delft >>>>>> <[email protected]> >> >> >> >> >> >> >>>>>> >>>>>> >>>>>> 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 >>>>>> <[email protected]> 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 > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFQ8FE+UxlJ7aRr7hoRApmAAKCNjwmHe8q5QpoFA9V3cSVtMwLqbgCgxwIa > xwICsaEtz3Phoe6uM2kJ308= > =fdKq > -----END PGP SIGNATURE----- -- Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713
