Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / asarnow/pyem issues and pull requests

#109 - Default to 1 for `ImageSizeZ`

Pull Request - State: open - Opened by brisvag over 1 year ago

#108 - np.int -> int

Pull Request - State: closed - Opened by i7878 over 1 year ago - 1 comment

#107 - module 'numpy' has no attribute 'int'

Issue - State: closed - Opened by i7878 over 1 year ago - 2 comments

#106 - rlnOriginX and rlnOriginY values are missing!!!

Issue - State: closed - Opened by fonsecareyna82 over 1 year ago - 3 comments

#105 - bug generating the .star file with numpy==1.24.3

Issue - State: closed - Opened by fonsecareyna82 over 1 year ago - 2 comments

#104 - Fix(parse cs): Remove '>' char from path fields

Pull Request - State: closed - Opened by arulths over 1 year ago - 3 comments

#103 - star.file format error using pyem

Issue - State: closed - Opened by mqcarba over 1 year ago - 4 comments

#102 - Converting exported `.cs` file includes`>` char in file paths

Issue - State: closed - Opened by arulths over 1 year ago - 1 comment

#101 - New `csparc2star` default for `--inverty` breaks existing workflows

Issue - State: closed - Opened by brisvag over 1 year ago - 1 comment

#99 - Use psi priori for filament angles

Pull Request - State: closed - Opened by brisvag almost 2 years ago - 1 comment

#98 - ValueError with missing 'rigid_motion/path'

Issue - State: open - Opened by asarnow almost 2 years ago - 1 comment

#97 - Duplicate axis error

Issue - State: closed - Opened by asarnow almost 2 years ago - 3 comments

#96 - Handle missing gain reference

Issue - State: open - Opened by asarnow almost 2 years ago

#95 - Missing rlnImageSizeZ possible

Issue - State: open - Opened by asarnow almost 2 years ago

#94 - Convert zernike parameters

Pull Request - State: open - Opened by GenevieveBuckley almost 2 years ago - 2 comments

#93 - Support patch motion export

Issue - State: closed - Opened by asarnow about 2 years ago - 1 comment

#92 - star.py --merge-fields does not work to merge rlnImageOriginalName

Issue - State: closed - Opened by THWeng about 2 years ago - 2 comments

#91 - star.py --merge-fields not working as expected.

Issue - State: closed - Opened by mbelouso about 2 years ago - 1 comment

#90 - Fix all deprecation warnings

Issue - State: open - Opened by asarnow about 2 years ago

#89 - Fix deprecation warning, must use log.warning() instead of log.warn()

Pull Request - State: closed - Opened by GenevieveBuckley about 2 years ago - 1 comment

#88 - Bugfix: Zernike CTF parameters

Pull Request - State: closed - Opened by GenevieveBuckley about 2 years ago - 3 comments

#87 - CTF metadata parameters

Pull Request - State: closed - Opened by GenevieveBuckley about 2 years ago - 4 comments

#86 - CTF parameters from cryosparc

Issue - State: open - Opened by GenevieveBuckley about 2 years ago - 7 comments

#85 - star2bild.py ValueError: unsupported format character ')' (0x29) at index 11

Issue - State: closed - Opened by Henry-946 about 2 years ago - 6 comments

#84 - TypeError: parse_cryosparc_2_cs() got an unexpected keyword argument 'invertx'

Issue - State: closed - Opened by ajcdurand over 2 years ago - 3 comments

#83 - Error converting a CS 3DClassification .cs file to .start

Issue - State: closed - Opened by fonsecareyna82 over 2 years ago - 7 comments

#82 - Want to import corrected movies from relion to CS

Issue - State: closed - Opened by forhadsaikot over 2 years ago - 1 comment

#81 - csparc2star.py default coordinate conversions are confusing

Issue - State: closed - Opened by asarnow over 2 years ago - 1 comment

#80 - Only one file at a time supported for CryoSPARC 0.6.5 .csv format”

Issue - State: closed - Opened by udeepka over 2 years ago - 3 comments

#78 - Import error csparc2star.py

Issue - State: closed - Opened by ghatzop over 2 years ago - 1 comment

#76 - new FRC function

Issue - State: open - Opened by AmazonRF over 2 years ago

#75 - make scripts to proper package and define entry point

Pull Request - State: open - Opened by thorstenwagner almost 3 years ago - 6 comments

#74 - Fix --copy-micrograph-coordinates by removing cryoSPARC UIDs from paths

Pull Request - State: closed - Opened by arulths almost 3 years ago - 1 comment

#72 - Additional fixes for #70

Pull Request - State: closed - Opened by kttn8769 about 3 years ago - 1 comment

#71 - Removing leading UIDs from cryoSPARC inputs

Issue - State: closed - Opened by asarnow about 3 years ago - 1 comment

#70 - csparc2star.py raises ValueError upon converting Downsample Particles job result

Issue - State: closed - Opened by kttn8769 about 3 years ago - 5 comments

#69 - Fix star2bild.py ValueError when using --sym

Pull Request - State: closed - Opened by kttn8769 about 3 years ago - 3 comments

#68 - Handle unaligned particles w/ Rodrigues vector (0, 0, 0)

Issue - State: closed - Opened by fonsecareyna82 over 3 years ago - 15 comments

#67 - metadata.py breaks with particles with 2D and 3D pose

Issue - State: closed - Opened by brisvag over 3 years ago - 4 comments

#66 - Release Update Request

Issue - State: closed - Opened by dorton21 over 3 years ago

#65 - star2bild.py ValueError when using --sym

Issue - State: closed - Opened by basantab over 3 years ago - 2 comments

#64 - Input & output

Issue - State: closed - Opened by EB-kim over 3 years ago - 1 comment

#63 - pffttw not found

Issue - State: closed - Opened by EB-kim over 3 years ago - 3 comments

#62 - csparc2star.py not working for Relion 3.0+?

Issue - State: closed - Opened by JeanMichelMoreau over 3 years ago - 1 comment

#61 - Issue in using csparc2star.py

Issue - State: closed - Opened by JeanMichelMoreau over 3 years ago

#60 - Add parsing for filament id

Pull Request - State: closed - Opened by brisvag almost 4 years ago - 7 comments

#59 - exception raised when dealing with cryosparc 3.0.1's passsthrough_particle.cs

Issue - State: closed - Opened by inter1965 almost 4 years ago - 3 comments

#58 - Bug in to_micrographs (star.py) and syntax warning in mrc.py

Pull Request - State: closed - Opened by FlyinTeller almost 4 years ago - 1 comment

#57 - Shifted coordinates upon transforming from .cs to .star

Issue - State: closed - Opened by aliahmad-a almost 4 years ago - 2 comments

#56 - Star.py error

Issue - State: closed - Opened by ketanm010 about 4 years ago - 1 comment

#55 - csparc2star.py --copy-micrographs-coordinates

Issue - State: closed - Opened by sunny1226 about 4 years ago - 3 comments

#54 - [simple inquiry] Is git pull enough to use the latest pyem

Issue - State: closed - Opened by kimdn about 4 years ago - 1 comment

#53 - csparc2star.py issue converting from .cs to .star

Issue - State: closed - Opened by jianhaoc about 4 years ago - 2 comments

#51 - csparc2star.py no ImageSize info

Issue - State: closed - Opened by sunny1226 over 4 years ago - 1 comment

#50 - csparc2star.py outputs invalid paths: "#@>path"

Issue - State: closed - Opened by aaronjolewis over 4 years ago - 3 comments

#49 - Make a PyPI or conda package?

Issue - State: closed - Opened by Guillawme over 4 years ago - 1 comment

#48 - Converted star file using csparc2star.py cannot work in relion-3.1

Issue - State: closed - Opened by sunny1226 over 4 years ago - 1 comment

#47 - star.py error

Issue - State: closed - Opened by mwieczo over 4 years ago - 2 comments

#46 - Importing 2D from cryosparc 2.15.0 back to relion 3.1

Issue - State: closed - Opened by biolifei over 4 years ago - 1 comment

#45 - par2star retain optics

Pull Request - State: closed - Opened by emgreen over 4 years ago

#44 - 3D refinement issue in Relion after exporting from cryosparc

Issue - State: closed - Opened by Jake4484 over 4 years ago - 3 comments
Labels: bug

#43 - Trouble using csparc2star.py

Issue - State: closed - Opened by olibclarke over 4 years ago - 1 comment

#42 - csparc2star.py trouble - still

Issue - State: closed - Opened by ic1062 over 4 years ago - 1 comment

#41 - Importing 2D from cryosparc 2.1.4 back to relion 3.1

Issue - State: closed - Opened by Omid1985 almost 5 years ago - 15 comments

#40 - Exporting particles to relion imports micrographs

Issue - State: closed - Opened by mtuijtel about 5 years ago - 1 comment

#39 - No module named pyem.geom

Issue - State: closed - Opened by domgutier about 5 years ago - 1 comment
Labels: question

#38 - ImportError: No module named pandas

Issue - State: closed - Opened by mtuijtel about 5 years ago - 2 comments
Labels: question

#37 - star.py fails on particles.star file with space before column labels

Issue - State: closed - Opened by andreanans about 5 years ago - 1 comment

#36 - Shorten float number format in star output

Pull Request - State: closed - Opened by Xbar over 5 years ago - 1 comment

#35 - Export particles coordinate

Issue - State: closed - Opened by wxh180 over 5 years ago - 1 comment

#34 - from cryosparc to relion

Issue - State: closed - Opened by Omid1985 over 5 years ago - 2 comments
Labels: question

#33 - Conflicting D symmetry conventions

Issue - State: closed - Opened by pconesa over 5 years ago - 7 comments
Labels: bug

#32 - Python version conflict

Issue - State: closed - Opened by sunny1226 over 5 years ago - 2 comments
Labels: enhancement

#31 - Update release branch

Pull Request - State: closed - Opened by asarnow over 5 years ago

#29 - New csparc2star.py error

Issue - State: closed - Opened by egiudice almost 6 years ago - 2 comments

#28 - TypeError in csparc2star.py

Issue - State: closed - Opened by attamatti almost 6 years ago - 1 comment

#27 - csparc2star.py ValueError: Columns must be same length as key

Issue - State: closed - Opened by sunny1226 almost 6 years ago - 4 comments

#26 - Convert cs to star

Issue - State: closed - Opened by wxh180 almost 6 years ago - 5 comments

#25 - Error running csparc2star.py

Issue - State: closed - Opened by hansenbry almost 6 years ago - 1 comment

#23 - Fix failure when reading star-files without rln-header

Pull Request - State: closed - Opened by dthirst almost 6 years ago - 1 comment

#22 - y-flip on the coordinates for relion3

Issue - State: closed - Opened by alburse about 6 years ago - 7 comments

#21 - Reverse x and y in cryosparc micrograph_shape array. Convert modf to round.

Pull Request - State: closed - Opened by turalaksel about 6 years ago - 9 comments

#20 - signature="(m),(m)->(m)") error on Linux

Issue - State: closed - Opened by evanseitz about 6 years ago - 1 comment

#19 - handling strings as bytes

Issue - State: closed - Opened by geoffwoollard about 6 years ago - 3 comments
Labels: enhancement

#18 - AttributeError

Issue - State: closed - Opened by pherepanov about 6 years ago - 2 comments

#17 - install problem

Issue - State: closed - Opened by istv01 about 6 years ago - 1 comment

#16 - Cryosparc 2 to star

Issue - State: closed - Opened by dhaselb about 6 years ago - 1 comment

#15 - install problem

Issue - State: closed - Opened by robinbinchen over 6 years ago - 2 comments

#14 - csparc2star.py

Issue - State: closed - Opened by xzhang1999 over 6 years ago - 4 comments

#13 - pyem algo module error with star.py

Issue - State: closed - Opened by domgutier over 6 years ago - 3 comments

#12 - fix python3 compatibility

Pull Request - State: closed - Opened by Xbar over 6 years ago

#11 - csparc2star.py - AttributeError: 'module' object has no attribute 'Relion'

Issue - State: closed - Opened by pherepanov over 6 years ago - 5 comments

#10 - csparc2star.py to be used for movie refinement

Issue - State: closed - Opened by aglape almost 7 years ago - 2 comments