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LBEM-CH / focus

High Throughput Electron Microscopy Image Processing Software
http://www.focus-em.org
GNU General Public License v2.0
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Making crystal from polygon #244

Closed EthanJUCB closed 5 years ago

EthanJUCB commented 5 years ago

Hi all,

I had a problem when I tried to make crystal from polygon. It happened to both the latest and the old version in Centos7.

======================================================================================================================================================================================================= ==== modifypolygon - to prepare the input data for boximage ===========================================================================================================================================

Using as original polygon file: 1837.44, 1837.44 ! X,Y dimensions of the original image, origin bottom left (0,0) 93, 2180 77, 1372 2660, 44 3221, 78 3171, 1570 188, 2196 108, 2176

##########################2dx_maskCrystal finished.########################### At line 30 of file /local0/hudson/jenkins/buildst01/jenkins/buildst01/workspace/focus_nightly_build/label/fedora/kernel/mrc/source/2dx_modifypolygon.for (unit = 11, file = 'selectionList.dat') Fortran runtime error: Bad integer for item 1 in list input

I checked 'selectionList.dat' , it looked normal, then I ran the 2dx_modifypolygon.exe in terminal. There was no response from this command. Other 2dx commands in /kernel/mrc/bin worked properly.

Any suggestions, many thanks.

Best Xi

rdrighetto commented 5 years ago

Dear Xi,

Sorry, I was not able to reproduce the issue. Could you please provide a screenshot of the polygon and the 'selectionList.dat' file?

Also, maybe this is a CentOS and/or gfortran issue from our continuous integration system. I will try to test the .rpm binary here. In the meantime, would it be possible for you to try e.g. the .deb version of the binary, or compile from source?

Or maybe @sthennin already knows this issue or a possible solution?

EthanJUCB commented 5 years ago

Hi Ricardo,

Thanks very much. Make polygon works now after I upgraded to the latest version using RPM. However, I had new issue when I came back to make FFT for the the masked image. Please see attached information.

Sure, I will try to build from source.

Best Xi

#################################2dx_fftrans##################################

############################################

Parameters requested by the Script

############################################ phaseori_done = n tempkeep = n imagename = mimage_2dx nonmaskimagename = image_2dx imagenumber = 0000002295 imagesidelength = 3300 realcell = 9,38 magnification = 89798.9 stepdigitizer = 5.0 calc_from_sample_pixel = y sample_pixel = 0.5568 realang = 90.0 phacon = 0.995 resmin = 200.0 resmax = 2.0 radlim = 35.0,35.0,0.0 generateperiodogram = n periodogramwindowsize = 512 periodogramnumsubsteps = 20 taperbeforefft = y crop = 1 crop_histogram = y crop_histogram_percent = 5 crop_histogram_stdev = 4.0 ctfcor_imode = 1 use_masked_image = y movie_inmovie = n movie_stackname = movie_aligned

############################################

Parameters from the Preferences settings

############################################ app_python = /usr/bin/python2.7 app_cadaver = /usr/bin/cadaver app_anaconda = /usr/bin/python2.7 dir_ccp4 = /home/xijiang/Downloads/ccp4-7.0 app_gawk = /usr/local/Cellar/gawk cuda_library = /usr/local/cuda/lib64 app_unblur = /usr/local/cina/unblur/unblur_1.0.2/bin/unblur_openmp_7_17_15.exe app_motioncor2 = /usr/local/cina/motioncor2/bin/motioncor2.exe app_gctf = /home/xijiang/Downloads/Gctf_v1.06/bin/Gctf-v1.06_sm_30_cu8.0_x86_64 app_ctffind = /home/xijiang/Downloads/CTFFIND4/bin/ctffind app_gautomatch = /usr/local/cina/Gautomatch/0.50_cuda7.5/bin/gautomatch dir_eman2 = /usr/local/EMAN2 dir_imod = /usr/local/IMOD dir_frealign = /home/xijiang/Downloads/frealign-2dx-master dir_relion = /usr/local/relion Microscope_Name = CryoEM Default_CS = 2.6 Default_KV = 300.0 Default_phase_shift_doit = n status_folder_update = n status_folder = none status_microscope = Titan status_refresh_rate = 0 status_webdav = http://my.server.com/files http://my.server.com/files website_blur_doit = y website_blurkernel = 7 SCRATCH_DISK = . FAST_DISK = . GPU_how_many = 4 GPU_to_use = 0 1 2 3 GPU_cycle = n MotionCor2_alone = y notify_email_admin = y notify_email_admin_adress = name@provider.com mailto:name@provider.com notify_last_minutes = 15 notify_delay_minutes = 60 notify_lastnumber = 50 notify_limit_mild = 30 notify_limit_severe = 15 flag_isdark_threshold = 0.1 flag_hasstripe_threshold = 38.0 flag_hastoohighdefocus_threshold = 7.0 flag_hastoolowdefocus_threshold = 0.2 flag_icinesstoohigh_threshold = 1.6 flag_drifttoohigh_threshold = 50.0 flag_astigmatismtoohigh_threshold = 0.03 flag_ctfresolutiontoobad_threshold = 8.0

#############################################

Now the remainder of the original script:

#############################################

++++++++++++++++++++++++++++++++ Initializing script environment ++++++++++++++++++++++++++++++++

Running the following shell: version tcsh 6.18.01 (Astron) 2012-02-14 (x86_64-unknown-linux) options wide,nls,dl,al,kan,sm,rh,color,filec

date = Tue Oct 8 11:07:32 PDT 2019 system = Linux bin_2dx = /opt/focus/kernel/mrc/bin proc_2dx = /opt/focus/scripts/proc ==== dir_eman2 = /usr/local/EMAN2 ===================================================================================================================================================================== ==== app_python = /usr/bin/python2.7 ================================================================================================================================================================== ==== app_anaconda = /usr/bin/python2.7 ================================================================================================================================================================ ==== dir_frealign = /home/xijiang/Downloads/frealign-2dx-master ======================================================================================================================================= ==== dir_relion = /usr/local/relion ===================================================================================================================================================================

======================================================================================================================================================================================================= ==== RELION installation directory not found. Is it installed ??? =====================================================================================================================================

======================================================================================================================================================================================================= ==== /usr/local/relion ================================================================================================================================================================================

======================================================================================================================================================================================================= ==== The location of RELION installation is defined in Preferences. ===================================================================================================================================

======================================================================================================================================================================================================= ==== Sourcing 2dx_init_files_sub.com http://2dx_init_files_sub.com/ ==================================================================================================================================================================

======================================================================================================================================================================================================= ==== Setting imagename to image_2dx.mrc ===============================================================================================================================================================

======================================================================================================================================================================================================= ==== Testing if image_2dx.mrc exists ==================================================================================================================================================================

======================================================================================================================================================================================================= ==== Copying image_2dx_raw.mrc onto image_2dx.mrc =====================================================================================================================================================

############################2dx_fftrans finished.############################# cp: ?image_2dx_raw.mrc? and ?image_2dx.mrc? are the same file

On Oct 8, 2019, at 9:29 AM, Ricardo Righetto notifications@github.com wrote:

Dear Xi,

Sorry, I was not able to reproduce the issue. Could you please provide a screenshot of the polygon and the 'selectionList.dat' file?

Also, maybe this is a CentOS and/or gfortran issue from our continuous integration issue. I will try to test the .rpm binary here. In the meantime, would it be possible for you to try e.g. the .deb version of the binary, or compile from source?

Or maybe @sthennin https://github.com/sthennin already knows this issue or a possible solution?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/C-CINA/focus/issues/244?email_source=notifications&email_token=AEVLNHEUCILXY7OPPUXPAETQNSYNNA5CNFSM4I5KQ3VKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAUZC7Q#issuecomment-539595134, or mute the thread https://github.com/notifications/unsubscribe-auth/AEVLNHHHTXF2ZNA4BM5TJGTQNSYNNANCNFSM4I5KQ3VA.

sthennin commented 5 years ago

Dear Xi, Your polygon file starts with a floating point number 1837.44, 1837.44 ! X,Y dimensions of the original image, origin bottom left (0,0) That is very odd. An image cannot have 1837.44 pixels in one row. How did you get these dimensions of the image file? Those should be integers. The program in charge to read that expects integers. I don't want to change that, since it would be important to verify where your polygon image dimensions come from. How did you get that file?

klhvorecny commented 5 years ago

Hello,

I am receiving the same error that Xi mentions above (see below for the text of the error). I'm running 2DXtal through the GUI. Running "Init Program" through "Get Lattice" works just fine. Under "Custom," I use "Mask Crystal from Polygon." The resulting masked image looks correct, but when I then rerun "Calculate FFTs," I get the error, "cp: 'image_2dx_raw.mrc' and 'image_2dx.mrc' are the same file"

Thanks for the help, Kelli

#################################2dx_fftrans##################################

############################################

Parameters requested by the Script

############################################ phaseori_done = n tempkeep = n imagename = mimage_2dx nonmaskimagename = image_2dx imagenumber = 0000000001 imagesidelength = 3808 realcell = 100.0,100.0 magnification = 10000 stepdigitizer = 1.9 calc_from_sample_pixel = y sample_pixel = 1.9 realang = 90.0 phacon = 0.995 resmin = 200.0 resmax = 4.0 radlim = 35.0,35.0,0.0 generateperiodogram = n periodogramwindowsize = 512 periodogramnumsubsteps = 20 taperbeforefft = y crop = 1 crop_histogram = y crop_histogram_percent = 5 crop_histogram_stdev = 4.0 ctfcor_imode = 1 use_masked_image = y movie_inmovie = n movie_stackname = movie_aligned

############################################

Parameters from the Preferences settings

############################################ app_python = /usr/bin/python app_cadaver = /usr/bin/cadaver app_anaconda = /usr/bin/python dir_ccp4 = /opt/applications/ccp4/7.0/ccp4-7.0 app_gawk = /usr/local/Cellar/gawk cuda_library = /usr/local/cuda/lib64 app_unblur = /usr/local/cina/unblur/unblur_1.0.2/bin/unblur_openmp_7_17_15.exe app_motioncor2 = /usr/local/cina/motioncor2/bin/motioncor2.exe app_gctf = /opt/applications/modulefiles/applications/gctf/1.06 app_ctffind = /opt/applications/ctf/4.1.10/bin/ctffind4 app_gautomatch = /usr/local/cina/Gautomatch/0.50_cuda7.5/bin/gautomatch dir_eman2 = /opt/applications/modulefiles/applications/eman dir_imod = /usr/local/IMOD dir_frealign = /opt/applications/modulefiles/applications/frealign dir_relion = /opt/applications/modulefiles/applications/relion Microscope_Name = CryoEM Default_CS = 2.7 Default_KV = 300.0 Default_phase_shift_doit = n status_folder_update = n status_folder = none status_microscope = Titan status_refresh_rate = 0 status_webdav = http://my.server.com/files website_blur_doit = y website_blurkernel = 7 SCRATCH_DISK = . FAST_DISK = . GPU_how_many = 4 GPU_to_use = 0 1 2 3 GPU_cycle = n MotionCor2_alone = y notify_email_admin = y notify_email_admin_adress = name@provider.com notify_last_minutes = 15 notify_delay_minutes = 60 notify_lastnumber = 50 notify_limit_mild = 30 notify_limit_severe = 15 flag_isdark_threshold = 0.1 flag_hasstripe_threshold = 38.0 flag_hastoohighdefocus_threshold = 7.0 flag_hastoolowdefocus_threshold = 0.2 flag_icinesstoohigh_threshold = 1.6 flag_drifttoohigh_threshold = 50.0 flag_astigmatismtoohigh_threshold = 0.03 flag_ctfresolutiontoobad_threshold = 8.0

#############################################

Now the remainder of the original script:

#############################################

++++++++++++++++++++++++++++++++ Initializing script environment ++++++++++++++++++++++++++++++++

Running the following shell: version tcsh 6.17.00 (Astron) 2009-07-10 (x86_64-unknown-linux) options wide,nls,dl,al,kan,sm,rh,color,filec

date = Mon Nov 4 10:10:37 PST 2019 system = Linux bin_2dx = /opt/applications/focus/3.5.0/gnu/kernel/mrc/bin proc_2dx = /opt/applications/focus/3.5.0/gnu/scripts/proc ==== dir_eman2 = /opt/applications/modulefiles/applications/eman ====================================================================================================================================== ==== app_python = /usr/bin/python ===================================================================================================================================================================== ==== app_anaconda = /usr/bin/python =================================================================================================================================================================== ==== dir_frealign = /opt/applications/modulefiles/applications/frealign =============================================================================================================================== ==== dir_relion = /opt/applications/modulefiles/applications/relion ===================================================================================================================================

======================================================================================================================================================================================================= ==== Sourcing 2dx_init_files_sub.com ==================================================================================================================================================================

======================================================================================================================================================================================================= ==== Setting imagename to image_2dx.mrc ===============================================================================================================================================================

======================================================================================================================================================================================================= ==== Testing if image_2dx.mrc exists ==================================================================================================================================================================

======================================================================================================================================================================================================= ==== Copying image_2dx_raw.mrc onto image_2dx.mrc =====================================================================================================================================================

############################2dx_fftrans finished.############################# cp: 'image_2dx_raw.mrc' and 'image_2dx.mrc' are the same file

sthennin commented 5 years ago

This should be fixed now. Please update to the latest version on GitHub. Thanks, Henning.

klhvorecny commented 5 years ago

That did the trick. Thank you, Kelli