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cryoem / eman2

A scientific image processing software suite with a focus on CryoEM and CryoET
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NameError: global name 'EMANVERSION' is not defined #137

Closed jianhaoc closed 6 years ago

jianhaoc commented 6 years ago

Hi specialists,

I am trying install EMAN2.2 (centos6 or centos7 version). But when I ran e2display.py and failed with a error as following.

$ e2display.py Traceback (most recent call last): File "/home/jianhaoc/s/EMAN22centos6/bin/e2display.py", line 34, in from EMAN2 import EMANVERSION, E2init, E2end, EMData, base_name, file_exists, EMArgumentParser ImportError: cannot import name EMANVERSION

I tried other programmes. e2proc3d.py is ok for both versions, but e2proc2d.py or e2reliontoeman.py didn't work for neither versions.

$ e2reliontoeman.py --help Traceback (most recent call last): File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 157, in main() File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 56, in main parser = EMArgumentParser(usage=usage,version=EMANVERSION) NameError: global name 'EMANVERSION' is not defined

$ e2proc2d.py --help Traceback (most recent call last): File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 1171, in main() File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 174, in main parser = EMArgumentParser(usage=usage,version=EMANVERSION) NameError: global name 'EMANVERSION' is not defined

Am I missing something? Thank you!

Regards, Jianhao

sludtke42 commented 6 years ago

Hi Jianhao, you reported a similar problem last month, and I suggested it was an issue with installing the CentOS7 version on a CentOS6 machine, then you said you tried a different computer and that machine was ok, and you never followed up on the original machine. The last time you reported the e2version.py output, which indicated this was the problem. This time you didn't include that.

Steven Ludtke, Ph.D. Charles C. Bell, Jr. Professor of Structural Biology Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem) Co-Director CIBR Center (www.bcm.edu/research/cibr) Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu) Baylor College of Medicine
sludtke@bcm.edu

On Oct 27, 2017, at 4:49 AM, jianhaoc notifications@github.com wrote:

Hi specialists,

I am trying install EMAN2.2 (centos6 or centos7 version). But when I ran e2display.py and failed with a error as following.

$ e2display.py Traceback (most recent call last): File "/home/jianhaoc/s/EMAN22centos6/bin/e2display.py", line 34, in from EMAN2 import EMANVERSION, E2init, E2end, EMData, base_name, file_exists, EMArgumentParser ImportError: cannot import name EMANVERSION

I tried other programmes. e2proc3d.py is ok for both versions, but e2proc2d.py or e2reliontoeman.py didn't work for neither versions.

$ e2reliontoeman.py --help Traceback (most recent call last): File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 157, in main() File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 56, in main parser = EMArgumentParser(usage=usage,version=EMANVERSION) NameError: global name 'EMANVERSION' is not defined

$ e2proc2d.py --help Traceback (most recent call last): File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 1171, in main() File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 174, in main parser = EMArgumentParser(usage=usage,version=EMANVERSION) NameError: global name 'EMANVERSION' is not defined

Am I missing something? Thank you!

Regards, Jianhao

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jianhaoc commented 6 years ago

Hi Steve Sorry for missing that. I also remember that, but googlegroup or gmail is unavailable these days. So I tried both these two versions. The detail informations are attached.

Regards, Jianhao

For centos6 version $ e2version.py EMAN 2.2 (GITHUB: 2017-09-20 00:31 - commit: None ) Your EMAN2 is running on: Linux-2.6.32-573.12.1.el6_lustre.x86_64-x86_64-with-centos-6.7-Final 2.6.32-573.12.1.el6_lustre.x86_64 Your Python version is: 2.7.13

For centos7 version $ e2version.py EMAN 2.2 (GITHUB: 2017-09-20 00:00 - commit: 4aa69dd ) Your EMAN2 is running on: Linux-2.6.32-573.12.1.el6_lustre.x86_64-x86_64-with-centos-6.7-Final 2.6.32-573.12.1.el6_lustre.x86_64 Your Python version is: 2.7.13

for centos6 version $ e2proc2d.py --help Traceback (most recent call last): File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 1171, in main() File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 174, in main parser = EMArgumentParser(usage=usage,version=EMANVERSION) NameError: global name 'EMANVERSION' is not defined

$ e2reliontoeman.py --help Traceback (most recent call last): File "/home/jianhaoc/s/EMAN22centos6/bin/e2reliontoeman.py", line 157, in main() File "/home/jianhaoc/s/EMAN22centos6/bin/e2reliontoeman.py", line 56, in main parser = EMArgumentParser(usage=usage,version=EMANVERSION) NameError: global name 'EMANVERSION' is not defined

$ e2proc3d.py --help Usage: e2proc3d.py [options] Generic 3-D image processing and file format conversion program. All EMAN2 recognized file formats accepted (see Wiki for list).

To create a new image, rather than reading from a file, specify ':<nx>:<ny>:<nz>:<value>'
as an input filename.

Examples:

Convert MRC format to HDF format:
e2proc3d.py test.mrc test.hdf

Apply a 10 A low-pass filter to a volume and write output to a new file:
e2proc3d.py threed.hdf threed.filt.hdf --process=filter.lowpass.gauss:cutoff_freq=0.1

Extract a reconstruction from a refinement directory as an HDF file usable with Chimera:
e2proc3d.py bdb:refine_02#threed_filt_04 map_02_04.hdf

Create a new 64x64x64 volume, initialize it as 1, then apply a hard spherical mask to 0:
e2proc3d.py :64:64:64:1 myvol.hdf --process mask.sharp:outer_radius=25

'e2help.py processors -v 2' for a detailed list of available procesors

Options: -h, --help show this help message and exit --medianshrink=n Downsamples the volume by a factor of n by computing the local median --meanshrink=n Downsamples the volume by a factor of n by computing the local average --meanshrinkbig=n Downsamples the volume by a factor of n without reading the entire volume into RAM. The output file (after shrinking) must fit into RAM. If specified, this must be the ONLY option on the command line. Any other options will be ignored. Output data type will match input data type. Works only on single image files, not stack files. --scale=n Rescales the image by 'n', generally used with clip option. --sym=SYM Symmetry to impose - choices are: c, d, h, tet, oct, icos --averager=AVERAGER Averager used for --average and --sym options --clip=x[,y,z[,xc,yc,zc]] Make the output have this size by padding/clipping. 1, 3 or 6 arguments. --fftclip=x, y, z Make the output have this size, rescaling by padding FFT. --process=processor_name:param1=value1:param2=value2 apply a processor named 'processorname' with all its parameters/values. --apix=APIX A/pixel for S scaling --origin=x, y, z Set the coordinates for the pixel (0,0,0) for Chimera. THIS HAS NO IMPACT ON IMAGE PROCESSING ! --mult=f Scales the densities by a fixed number in the output --multfile=MULTFILE Multiplies the volume by another volume of identical size. This can be used to apply masks, etc. --matchto=MATCHTO Match filtration of input volume to this specified volume. --outmode=OUTMODE All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (int8, int16, int32, uint8, uint16, uint32). Values are rescaled to fill MIN-MAX range. --outnorescale If specified, floating point values will not be rescaled when writing data as integers. Values outside of range are truncated. --mrc16bit (deprecated, use --outmode instead) output as 16 bit MRC file --mrc8bit (deprecated, use --outmode instead) output as 8 bit MRC file --add=f Adds a constant 'f' to the densities --addfile=ADDFILE Adds the volume to another volume of identical size --calcfsc=with input Calculate a FSC curve between two models. Output is a txt file. This option is the name of the second volume. --filtertable=FILTERTABLE Applies a 2 column (S,amp) file as a filter in Fourier space, assumed 0 outside the defined range. --calcsf=outputfile Calculate a radial structure factor. Must specify apix. --calcradial=CALCRADIAL Calculate the radial density by shell. Output file becomes a text file. 0 - mean amp, 2 - min, 3 - max, 4

shadowwalkersb commented 6 years ago

@jianhaoc , you seem to be on CentOS6, so centos7 version, probably, won't run. When your centos6 installation is active, can you provide the output for the following?

conda info -a
which -a e2proc2d.py
e2proc2d.py --help
jianhaoc commented 6 years ago

Hi @shadowwalkersb , Please see below. Besides what you ask to do, I also tried e2reliontoeman.py. Thank you.

$ conda info -a Current conda install:

           platform : linux-64
      conda version : 4.3.21
   conda is private : False
  conda-env version : 4.3.21
conda-build version : 2.1.15
     python version : 2.7.13.final.0
   requests version : 2.14.2
   root environment : /home/jianhaoc/s/eman22centos6_20171028  (writable)
default environment : /home/jianhaoc/s/eman22centos6_20171028
   envs directories : /home/jianhaoc/s/eman22centos6_20171028/envs
                      /home/jianhaoc/.conda/envs
      package cache : /home/jianhaoc/s/eman22centos6_20171028/pkgs
                      /home/jianhaoc/.conda/pkgs
       channel URLs : https://repo.continuum.io/pkgs/free/linux-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/r/linux-64
                      https://repo.continuum.io/pkgs/r/noarch
                      https://repo.continuum.io/pkgs/pro/linux-64
                      https://repo.continuum.io/pkgs/pro/noarch
                      https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64
                      https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
        config file : /home/jianhaoc/.condarc
         netrc file : None
       offline mode : False
         user-agent : conda/4.3.21 requests/2.14.2 CPython/2.7.13 Linux/2.6.32-573.12.1.el6_lustre.x86_64 CentOS/6.7 glibc/2.12    
            UID:GID : 1012:1012

conda environments:

# root * /home/jianhaoc/s/eman22centos6_20171028

sys.version: 2.7.13 | packaged by conda-forge | (defa... sys.prefix: /home/jianhaoc/s/eman22centos6_20171028 sys.executable: /home/jianhaoc/s/eman22centos6_20171028/bin/python conda location: /home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/conda conda-build: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-build conda-convert: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-convert conda-develop: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-develop conda-env: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-env conda-index: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-index conda-inspect: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-inspect conda-metapackage: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-metapackage conda-render: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-render conda-sign: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-sign conda-skeleton: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-skeleton conda-verify: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-verify user site dirs:

CIO_TEST: CONDA_DEFAULT_ENV: CONDA_ENVS_PATH: LD_LIBRARY_PATH: /home/programs/openmpi/lib:/home/programs/fltk/lib:/home/programs/fftw/lib:/home/jianhaoc/s/gcc/gcc-7.2.0/gmp-6.1.0/build/lib:/home/jianhaoc/s/gcc/gcc-7.2.0/mpfr-3.1.4/build/lib:/home/jianhaoc/s/gcc/gcc-7.2.0/mpc-1.0.3/build/lib PATH: /home/jianhaoc/s/eman22centos6_20171028/bin:/home/jianhaoc/s/gcc/gcc-7.2.0/build/bin:/home/jianhaoc/s/gcc/gcc-7.2.0/gmp-6.1.0/build::/home/programs/tools:/home/jianhaoc/s/relion/build/bin:/home/programs/openmpi/bin:/usr/local/bin:/usr/local/sbin:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/iperf3/bin:/usr/local/rrdtool/bin:/usr/local/ganglia/bin:/usr/local/ganglia/sbin PYTHONHOME: PYTHONPATH:

WARNING: could not import _license.show_info

try:

$ conda install -n root _license

$ which -a e2proc2d.py ~/s/eman22centos6_20171028/bin/e2proc2d.py

$ e2proc2d.py --help usage: e2proc2d.py [options] ... 

MRC stack files MUST use the .mrcs extension to be treated as a set of 2-D images (or you must 
use one of the --threed* options)

If there is more than one input file, then outputfile is a pattern, where @
in the pattern is replaced by the input file base name (minus any extension).

Generic 2-D image processing and file format conversion program. Acts on stacks of 2-D images
(multiple images in one file). All EMAN2 recognized file formats accepted (see Wiki for list).

You can create a new 2-D or 3-D image from scratch instead of reading from a file by specifying 
':<nx>:<ny>:<expression_in_x_y>' or ':<nx>:<ny>:<nz>:<expression_in_x_y_z>' as an input filename,
where 0 <= x < nx, 0 <= y < ny, 0 <= z < nz, and the expression can be just a number.

    If performing certain operations which do not require an output file, specify "none" as the output file.

Examples:

convert IMAGIC format test.hed to HDF format:
e2proc2d.py test.hed test.hdf

convert all MRC format files in current directory to HDF format:
e2proc2d.py *.mrc @.hdf

convert a 'set' (.lst file) to an MRC stack file:
e2proc2d.py sets/myset.lst myset.mrcs

create a new image, initialized with 1.0, then mask it:
e2proc2d.py :128:128:1 mymask.hdf --process mask.soft:outer_radius=50

apply a 10 A low-pass filter to a stack of particles downsample the particles by a factor of 2
and write output to a new file.
e2proc2d.py ptcl.hdf ptcl.filt.hdf --process filter.lowpass.gauss:cutoff_freq=0.1 --meanshrink 2

'e2help.py processors -v 2' for a detailed list of available procesors

positional arguments: postionalargs

optional arguments: -h, --help show this help message and exit --version show program's version number and exit --apix APIX A/pixel for S scaling --average Averages all input images (without alignment) and writes a single output image --averager AVERAGER If --average is specified, this is the averager to use (e2help.py averager). Default=mean --calcsf outputfile calculate a radial structure factor for the image and write it to the output file, must specify apix. divide into angular bins --calccont Compute the low resolution azimuthal contrast of each image and put it in the header as eval_contrast_lowres. Larger values imply more 'interesting' images. --clip xsize,ysize Specify the output size in pixels xsize,ysize[,xcenter,ycenter], images can be made larger or smaller. --exclude exclude-list-file Excludes image numbers in EXCLUDE file --fftavg filename Incoherent Fourier average of all images and write a single power spectrum image --process processor_name:param1=value1:param2=value2 apply a processor named 'processorname' with all its parameters/values. --mult k Multiply image by a constant. mult=-1 to invert contrast. --add f Adds a constant 'f' to the densities --addfile ADDFILE Adds the volume to another volume of identical size --first n the first image in the input to process [0 - n-1]) --last n the last image in the input to process --list listfile Works only on the image numbers in LIST file --select selectname Works only on the images in named selection set from bdb:select --inplace Output overwrites input, USE SAME FILENAME, DO NOT 'clip' images. --interlv interleave-file Specifies a 2nd input file. Output will be 2 files interleaved. --extractboxes Extracts box locations from the image header to produce a set of .box files for only the particles in the .lst files --meanshrink n Reduce an image size by an integral (1.5 also allowed) scaling factor using average. eg - 2 will reduce image size to 1/2. Clip is not required. --medianshrink n Reduce an image size by an integral scaling factor, uses median filter. eg - 2 will reduce image size to 1/2. Clip is not required. --fouriershrink n Reduce an image size by an arbitrary scaling factor by clipping in Fourier space. eg - 2 will reduce image size to 1/2. --mraprep this is an experimental option --outmode OUTMODE All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (float, int8, int16, int32, uint8, uint16, uint32). Values are rescaled to fill MIN-MAX range. --outnorescale If specified, floating point values will not be rescaled when writing data as integers. Values outside of range are truncated. --mrc16bit (deprecated, use --outmode instead) output as 16 bit MRC file --mrc8bit (deprecated, use --outmode instead) output as 8 bit MRC file --fixintscaling FIXINTSCALING When writing to an 8 or 16 bit integer format the data must be scaled. 'noscale' will assume the pixel values are already correct, 'sane' will pick a good range, a number will set the range to mean+=sigmanumber --multfile MULTFILE Multiplies the volume by another volume of identical size. This can be used to apply masks, etc. --norefs Skip any input images which are marked as references (usually used with classes.) --outtype image-type output image format, 'mrc', 'imagic', 'hdf', etc. if specify spidersingle will output single 2D image rather than 2D stack. --radon Do Radon transform --randomize RANDOMIZE Randomly rotate/translate the image. Specify: da,dxy,flip da is a uniform distribution over +-da degrees, dxy is a uniform distribution on x/y, if flip is 1, random handedness changes will occur --rotavg Compute the 1-D rotational average of each image as a final step before writing the output --rotate ROTATE Rotate clockwise (in degrees) --rfp this is an experimental option --fp FP This generates rotational/translational 'footprints' for each input particle, the number indicates which algorithm to use (0-6) --scale f Scale by specified scaling factor. Clip must also be specified to change the dimensions of the output map. --anisotropic ANISOTROPIC Anisotropic scaling, stretches on one axis and compresses the orthogonal axis. Specify amount,angle. See e2evalrefine --selfcl steps mode steps mode Output file will be a 180x180 self-common lines map for each image. --setsfpairs Applies the radial structure factor of the 1st image to the 2nd, the 3rd to the 4th, etc --split n Splits the input file into a set of n output files --translate TRANSLATE Translate by x,y pixels --headertransform HEADERTRANSFORM This will take the xform.align2d header value from each particle, and apply it. Pass 0 to perform the transform or 1 to perform the inverse. --verbose n, -v n verbose level [0-9], higner number means higher level of verboseness --plane ['xy', 'yx', 'xz', 'zx', 'yz', 'yz'] Change the plane of image processing, useful for processing 3D mrcs as 2D images. --writejunk Writes the image even if its sigma is 0. --swap Swap the byte order --threed2threed Process 3D image as a stack of 2D slices, then output as a 3D image --threed2twod Process 3D image as a stack of 2D slices, then output as a 2D stack --twod2threed Process a stack of 2D images, then output as a 3D image. --unstacking Process a stack of 2D images, then output a a series of numbered single image files --ppid PPID Set the PID of the parent process, used for cross platform PPID --step STEP Specify ,. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles --parallel PARALLEL, -P PARALLEL Run in parallel, specify type:n=:option:option

$ e2reliontoeman.py --apix 2.5 --verbose 9 --refinedefocus p.star Parsing STAR file Traceback (most recent call last): File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 567, in open_db try : ret=JSDict(path) File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 638, in init self.sync() File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 689, in sync file_lock(jfile,readonly=False) File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 210, in file_lock else : fcntl.lockf(fileobj.fileno(),fcntl.LOCK_EX) IOError: [Errno 38] Function not implemented

Traceback (most recent call last): File "/home/jianhaoc/s/eman22centos6_20171028/bin/e2reliontoeman.py", line 157, in main() File "/home/jianhaoc/s/eman22centos6_20171028/bin/e2reliontoeman.py", line 93, in main prj=js_open_dict("info/project.json") File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 73, in js_open_dict return JSDict.open_db(url) File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 572, in open_db raise Exception,"Unable to open "+path Exception: Unable to open info/project.json

sludtke42 commented 6 years ago

Hi Jianhao, did we go through this once before? Maybe it was someone else... The error you are seeing there:

indicates that the disk you have your project on does not support file locking, which is critical to maintain file integrity. This usually happens with poorly configured remote filesystems, or external hard drives with old windows filesystems (not sure if this has that problem).

While shared filesystems can be fine when configured properly, in most cases they will be much slower than local storage (internal hard drive/RAID). External "portable" hard drives should never be used directly for data processing or as the only long term copy of your data, as their failure rate is MUCH higher than internal drives, they are even slower than remote filesystems in most cases, and (if they are USB) tend to have transitory I/O issues which can lead to jobs crashing. You may successfully get away with this approach for a while, but you are just asking for disaster.

Anyway, if this is your problem, I would strongly encourage you to copy your project onto internal storage on the computer and do your processing there, using the external drive or remote storage for backups.

Steven Ludtke, Ph.D. Charles C. Bell, Jr. Professor of Structural Biology Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochemhttp://www.bcm.edu/biochem) Co-Director CIBR Center (www.bcm.edu/research/cibrhttp://www.bcm.edu/research/cibr) Co-Director National Center For Macromolecular Imaging (ncmi.bcm.eduhttp://ncmi.bcm.edu/) Baylor College of Medicine sludtke@bcm.edumailto:sludtke@bcm.edu

On Oct 31, 2017, at 3:20 AM, jianhaoc notifications@github.com<mailto:notifications@github.com> wrote:

Hi @shadowwalkersbhttps://github.com/shadowwalkersb , Please see below. Besides what you ask to do, I also tried e2reliontoeman.py. Thank you.

$ conda info -a Current conda install:

       platform : linux-64
  conda version : 4.3.21

conda is private : False conda-env version : 4.3.21 conda-build version : 2.1.15 python version : 2.7.13.final.0 requests version : 2.14.2 root environment : /home/jianhaoc/s/eman22centos6_20171028 (writable) default environment : /home/jianhaoc/s/eman22centos6_20171028 envs directories : /home/jianhaoc/s/eman22centos6_20171028/envs /home/jianhaoc/.conda/envs package cache : /home/jianhaoc/s/eman22centos6_20171028/pkgs /home/jianhaoc/.conda/pkgs channel URLs : https://repo.continuum.io/pkgs/free/linux-64 https://repo.continuum.io/pkgs/free/noarch https://repo.continuum.io/pkgs/r/linux-64 https://repo.continuum.io/pkgs/r/noarch https://repo.continuum.io/pkgs/pro/linux-64 https://repo.continuum.io/pkgs/pro/noarch https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch config file : /home/jianhaoc/.condarc netrc file : None offline mode : False user-agent : conda/4.3.21 requests/2.14.2 CPython/2.7.13 Linux/2.6.32-573.12.1.el6_lustre.x86_64 CentOS/6.7 glibc/2.12 UID:GID : 1012:1012

conda environments:

root * /home/jianhaoc/s/eman22centos6_20171028

sys.version: 2.7.13 | packaged by conda-forge | (defa... sys.prefix: /home/jianhaoc/s/eman22centos6_20171028 sys.executable: /home/jianhaoc/s/eman22centos6_20171028/bin/python conda location: /home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/conda conda-build: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-build conda-convert: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-convert conda-develop: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-develop conda-env: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-env conda-index: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-index conda-inspect: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-inspect conda-metapackage: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-metapackage conda-render: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-render conda-sign: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-sign conda-skeleton: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-skeleton conda-verify: /home/jianhaoc/s/eman22centos6_20171028/bin/conda-verify user site dirs:

CIO_TEST: CONDA_DEFAULT_ENV: CONDA_ENVS_PATH: LD_LIBRARY_PATH: /home/programs/openmpi/lib:/home/programs/fltk/lib:/home/programs/fftw/lib:/home/jianhaoc/s/gcc/gcc-7.2.0/gmp-6.1.0/build/lib:/home/jianhaoc/s/gcc/gcc-7.2.0/mpfr-3.1.4/build/lib:/home/jianhaoc/s/gcc/gcc-7.2.0/mpc-1.0.3/build/lib PATH: /home/jianhaoc/s/eman22centos6_20171028/bin:/home/jianhaoc/s/gcc/gcc-7.2.0/build/bin:/home/jianhaoc/s/gcc/gcc-7.2.0/gmp-6.1.0/build::/home/programs/tools:/home/jianhaoc/s/relion/build/bin:/home/programs/openmpi/bin:/usr/local/bin:/usr/local/sbin:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/iperf3/bin:/usr/local/rrdtool/bin:/usr/local/ganglia/bin:/usr/local/ganglia/sbin PYTHONHOME: PYTHONPATH:

WARNING: could not import _license.show_info

try: $ conda install -n root _license

$ which -a e2proc2d.py ~/s/eman22centos6_20171028/bin/e2proc2d.py

$ e2proc2d.py --help usage: e2proc2d.py [options] ...

MRC stack files MUST use the .mrcs extension to be treated as a set of 2-D images (or you must use one of the --threed* options)

If there is more than one input file, then outputfile is a pattern, where @ in the pattern is replaced by the input file base name (minus any extension).

Generic 2-D image processing and file format conversion program. Acts on stacks of 2-D images (multiple images in one file). All EMAN2 recognized file formats accepted (see Wiki for list).

You can create a new 2-D or 3-D image from scratch instead of reading from a file by specifying ':::' or '::::' as an input filename, where 0 <= x < nx, 0 <= y < ny, 0 <= z < nz, and the expression can be just a number.

If performing certain operations which do not require an output file, specify "none" as the output file.

Examples:

convert IMAGIC format test.hed to HDF format: e2proc2d.py test.hed test.hdf

convert all MRC format files in current directory to HDF format: e2proc2d.py *.mrc @.hdf

convert a 'set' (.lst file) to an MRC stack file: e2proc2d.py sets/myset.lst myset.mrcs

create a new image, initialized with 1.0, then mask it: e2proc2d.py :128:128:1 mymask.hdf --process mask.soft:outer_radius=50

apply a 10 A low-pass filter to a stack of particles downsample the particles by a factor of 2 and write output to a new file. e2proc2d.py ptcl.hdf ptcl.filt.hdf --process filter.lowpass.gauss:cutoff_freq=0.1 --meanshrink 2

'e2help.py processors -v 2' for a detailed list of available procesors

positional arguments: postionalargs

optional arguments: -h, --help show this help message and exit --version show program's version number and exit --apix APIX A/pixel for S scaling --average Averages all input images (without alignment) and writes a single output image --averager AVERAGER If --average is specified, this is the averager to use (e2help.py averager). Default=mean --calcsf outputfile calculate a radial structure factor for the image and write it to the output file, must specify apix. divide into angular bins --calccont Compute the low resolution azimuthal contrast of each image and put it in the header as eval_contrast_lowres. Larger values imply more 'interesting' images. --clip xsize,ysize Specify the output size in pixels xsize,ysize[,xcenter,ycenter], images can be made larger or smaller. --exclude exclude-list-file Excludes image numbers in EXCLUDE file --fftavg filename Incoherent Fourier average of all images and write a single power spectrum image --process processor_name:param1=value1:param2=value2 apply a processor named 'processorname' with all its parameters/values. --mult k Multiply image by a constant. mult=-1 to invert contrast. --add f Adds a constant 'f' to the densities --addfile ADDFILE Adds the volume to another volume of identical size --first n the first image in the input to process [0 - n-1]) --last n the last image in the input to process --list listfile Works only on the image numbers in LIST file --select selectname Works only on the images in named selection set from bdb:select --inplace Output overwrites input, USE SAME FILENAME, DO NOT 'clip' images. --interlv interleave-file Specifies a 2nd input file. Output will be 2 files interleaved. --extractboxes Extracts box locations from the image header to produce a set of .box files for only the particles in the .lst files --meanshrink n Reduce an image size by an integral (1.5 also allowed) scaling factor using average. eg - 2 will reduce image size to 1/2. Clip is not required. --medianshrink n Reduce an image size by an integral scaling factor, uses median filter. eg - 2 will reduce image size to 1/2. Clip is not required. --fouriershrink n Reduce an image size by an arbitrary scaling factor by clipping in Fourier space. eg - 2 will reduce image size to 1/2. --mraprep this is an experimental option --outmode OUTMODE All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (float, int8, int16, int32, uint8, uint16, uint32). Values are rescaled to fill MIN-MAX range. --outnorescale If specified, floating point values will not be rescaled when writing data as integers. Values outside of range are truncated. --mrc16bit (deprecated, use --outmode instead) output as 16 bit MRC file --mrc8bit (deprecated, use --outmode instead) output as 8 bit MRC file --fixintscaling FIXINTSCALING When writing to an 8 or 16 bit integer format the data must be scaled. 'noscale' will assume the pixel values are already correct, 'sane' will pick a good range, a number will set the range to mean+=sigmanumber --multfile MULTFILE Multiplies the volume by another volume of identical size. This can be used to apply masks, etc. --norefs Skip any input images which are marked as references (usually used with classes.) --outtype image-type output image format, 'mrc', 'imagic', 'hdf', etc. if specify spidersingle will output single 2D image rather than 2D stack. --radon Do Radon transform --randomize RANDOMIZE Randomly rotate/translate the image. Specify: da,dxy,flip da is a uniform distribution over +-da degrees, dxy is a uniform distribution on x/y, if flip is 1, random handedness changes will occur --rotavg Compute the 1-D rotational average of each image as a final step before writing the output --rotate ROTATE Rotate clockwise (in degrees) --rfp this is an experimental option --fp FP This generates rotational/translational 'footprints' for each input particle, the number indicates which algorithm to use (0-6) --scale f Scale by specified scaling factor. Clip must also be specified to change the dimensions of the output map. --anisotropic ANISOTROPIC Anisotropic scaling, stretches on one axis and compresses the orthogonal axis. Specify amount,angle. See e2evalrefine --selfcl steps mode steps mode Output file will be a 180x180 self-common lines map for each image. --setsfpairs Applies the radial structure factor of the 1st image to the 2nd, the 3rd to the 4th, etc --split n Splits the input file into a set of n output files --translate TRANSLATE Translate by x,y pixels --headertransform HEADERTRANSFORM This will take the xform.align2d header value from each particle, and apply it. Pass 0 to perform the transform or 1 to perform the inverse. --verbose n, -v n verbose level [0-9], higner number means higher level of verboseness --plane ['xy', 'yx', 'xz', 'zx', 'yz', 'yz'] Change the plane of image processing, useful for processing 3D mrcs as 2D images. --writejunk Writes the image even if its sigma is 0. --swap Swap the byte order --threed2threed Process 3D image as a stack of 2D slices, then output as a 3D image --threed2twod Process 3D image as a stack of 2D slices, then output as a 2D stack --twod2threed Process a stack of 2D images, then output as a 3D image. --unstacking Process a stack of 2D images, then output a a series of numbered single image files --ppid PPID Set the PID of the parent process, used for cross platform PPID --step STEP Specify ,. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles --parallel PARALLEL, -P PARALLEL Run in parallel, specify type:n=:option:option

$ e2reliontoeman.py --apix 2.5 --verbose 9 --refinedefocus p.star Parsing STAR file Traceback (most recent call last): File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 567, in open_db try : ret=JSDict(path) File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 638, in init self.sync() File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 689, in sync file_lock(jfile,readonly=False) File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 210, in file_lock else : fcntl.lockf(fileobj.fileno(),fcntl.LOCK_EX) IOError: [Errno 38] Function not implemented

Traceback (most recent call last): File "/home/jianhaoc/s/eman22centos6_20171028/bin/e2reliontoeman.py", line 157, in main() File "/home/jianhaoc/s/eman22centos6_20171028/bin/e2reliontoeman.py", line 93, in main prj=js_open_dict("info/project.json") File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 73, in js_open_dict return JSDict.open_db(url) File "/home/jianhaoc/s/eman22centos6_20171028/lib/python2.7/site-packages/EMAN2jsondb.py", line 572, in open_db raise Exception,"Unable to open "+path Exception: Unable to open info/project.json

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/cryoem/eman2/issues/137#issuecomment-340680393, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJ6i6jJWlhU4AB4yblZ9YfWWGXuH33Zuks5sxso0gaJpZM4QIz0c.

Steven Ludtke, Ph.D. Charles C. Bell, Jr. Professor of Structural Biology Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochemhttp://www.bcm.edu/biochem) Co-Director CIBR Center (www.bcm.edu/research/cibrhttp://www.bcm.edu/research/cibr) Co-Director National Center For Macromolecular Imaging (ncmi.bcm.eduhttp://ncmi.bcm.edu) Baylor College of Medicine sludtke@bcm.edumailto:sludtke@bcm.edu

jianhaoc commented 6 years ago

Hi @sludtke42 , Thank you for reminding me about that. Because I cann't access to the EMAN googlegroup these days to find my question back, I asked it again here. What a pity the shared filesystems are unavailable for EMAN2.

sludtke42 commented 6 years ago

EMAN does support shared filesystems IF they are properly configured to support file locking. This does exclude certain types of old filesystems which don't support this concept at all.

Steven Ludtke, Ph.D. Charles C. Bell, Jr. Professor of Structural Biology Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochemhttp://www.bcm.edu/biochem) Co-Director CIBR Center (www.bcm.edu/research/cibrhttp://www.bcm.edu/research/cibr) Co-Director National Center For Macromolecular Imaging (ncmi.bcm.eduhttp://ncmi.bcm.edu/) Baylor College of Medicine sludtke@bcm.edumailto:sludtke@bcm.edu

On Nov 1, 2017, at 9:22 AM, jianhaoc notifications@github.com<mailto:notifications@github.com> wrote:

Hi @sludtke42https://github.com/sludtke42 , Thank you for reminding me about that. Because I cann't access to the EMAN googlegroup these days to find my question back, I asked it again here. What a pity the shared filesystems are unavailable for EMAN2.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/cryoem/eman2/issues/137#issuecomment-341104503, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJ6i6k5saEzBx1OMWJEW1eXExUovQQ0Lks5syHCegaJpZM4QIz0c.

Steven Ludtke, Ph.D. Charles C. Bell, Jr. Professor of Structural Biology Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochemhttp://www.bcm.edu/biochem) Co-Director CIBR Center (www.bcm.edu/research/cibrhttp://www.bcm.edu/research/cibr) Co-Director National Center For Macromolecular Imaging (ncmi.bcm.eduhttp://ncmi.bcm.edu) Baylor College of Medicine sludtke@bcm.edumailto:sludtke@bcm.edu

jianhaoc commented 6 years ago

Sorry for missing your meaning again. I meant my filesystem might be not setup properly.

shadowwalkersb commented 6 years ago

Is there anything else to do here? Can this issue be closed?

jianhaoc commented 6 years ago

Hi,

I turned to another computer without shared filesystems.

regards, Jianhao

2018-05-01 6:13 GMT+08:00 shadow_walker notifications@github.com:

Is there anything else to do here? Can this issue be closed?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/cryoem/eman2/issues/137#issuecomment-385544703, or mute the thread https://github.com/notifications/unsubscribe-auth/AfGoDenHvdWkYb--eLK7N4t_pTGhbP9lks5tt4ySgaJpZM4QIz0c .