Ecosyste.ms: Issues

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GitHub / ccpem/mrcfile issues and pull requests

#62 - fix overflow errors when opening files bigger than np.int32.max bytes

Pull Request - State: closed - Opened by sroet 4 months ago - 3 comments

#61 - Fix overflow error when file size is large

Pull Request - State: closed - Opened by hanjinliu 5 months ago - 3 comments

#60 - Test failures with NumPy 2.0.0rc2

Issue - State: closed - Opened by mgorny 6 months ago - 5 comments

#59 - Origin in header is read-only

Issue - State: closed - Opened by alisterburt 10 months ago - 9 comments

#58 - Writing/reading extended header seems to be broken in latest version

Issue - State: open - Opened by jmp1985 10 months ago - 5 comments

#57 - How to use header information

Issue - State: closed - Opened by XiaoChen1992 about 1 year ago - 1 comment

#56 - Mismatch in supported modes between documentation and code

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

#54 - failed to read FEI2 ext header with mrcfile 1.4.3

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

#53 - test_data_is_not_read_if_dimensions_are_too_huge fails on i586

Issue - State: closed - Opened by pgajdos over 1 year ago - 7 comments

#52 - Extended header unused space fix

Pull Request - State: closed - Opened by dagewa over 1 year ago - 2 comments

#51 - bug: possibility of writing invalid headers yielding unreadable files

Issue - State: open - Opened by alisterburt over 1 year ago - 7 comments

#49 - Tests fail with Python 3.11 and Numpy 1.24.1: AssertionError

Issue - State: closed - Opened by s3v- almost 2 years ago - 11 comments

#48 - [Feature request] Ability to read from IOStream object directly

Issue - State: closed - Opened by ireneusz-ptak almost 2 years ago - 1 comment

#47 - imod file with unrecognized machine stamp

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

#45 - Option to calculate header.rms in float32?

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

#44 - Unable to fix mrc file header

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

#43 - Add helper functions for handling header labels

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

#42 - `mrcfile.write()` cannot be used with `pathlib.Path` objects

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

#41 - Test failures with Python 3.11

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

#40 - Bump numpy from 1.19.5 to 1.22.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#39 - module 'mrcfile' has no attribute 'read'

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

#38 - Gemmi vs mrcfile - values of some voxels are not equal

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

#37 - Allow the extended header to be set in the constructor of the new_mmap

Pull Request - State: closed - Opened by jmp1985 over 2 years ago - 1 comment

#36 - Don't issue warnings for complex valued mrcfiles

Pull Request - State: closed - Opened by jmp1985 over 2 years ago - 2 comments

#35 - 8 test failures on s390x

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

#34 - Opening a new mmap with an extended header is slow

Issue - State: closed - Opened by jmp1985 over 2 years ago - 1 comment

#33 - Complex valued data in mrcfile gives warnings.

Issue - State: closed - Opened by jmp1985 over 2 years ago - 1 comment

#32 - slightly change validate() to support changing permissiveness

Pull Request - State: closed - Opened by luke-c-sargent over 2 years ago - 2 comments

#31 - Permissive validation causes memory errors

Issue - State: closed - Opened by luke-c-sargent over 2 years ago - 2 comments

#30 - add `mrcfile.write()`

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

#29 - add `mrcfile.read()`

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

#28 - Proposal: `mrcfile.read()` and `mrcfile.write()`

Issue - State: closed - Opened by alisterburt almost 3 years ago - 9 comments

#27 - Correction of the usage guidelines

Issue - State: closed - Opened by MohamadHarastani almost 3 years ago - 1 comment

#26 - writing voxels sizes

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

#25 - Having trouble while saving the image into .TIF

Issue - State: closed - Opened by Yuvi-416 over 3 years ago - 4 comments

#24 - Fei2 header

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

#23 - mx,my and mz potentially being set wrong

Issue - State: open - Opened by Ryan-Pye about 4 years ago - 1 comment

#22 - commands do not support a --help option

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

#21 - Modify `n*start`

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

#20 - ValueError: cannot set WRITEABLE flag to True of this array

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

#19 - Error when opening MotionCor2 output

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

#18 - accessing specific slice from a memmap

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

#17 - AttributeError: module 'mrcfile' has no attribute 'open

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

#16 - Is there any way this can be used in a lazy way?

Issue - State: closed - Opened by markbasham about 5 years ago - 2 comments

#15 - ValueError: zero-size array to reduction operation minimum which has no identity

Issue - State: closed - Opened by pjpjq about 5 years ago - 13 comments

#14 - MAP_ID should match "MAP", not "MAP "

Pull Request - State: closed - Opened by milliams over 5 years ago - 3 comments

#13 - Errors when running against numpy 1.16

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

#12 - Fix list of valid extended header types

Pull Request - State: closed - Opened by kohr-h about 6 years ago - 2 comments

#11 - FEI extended header implementation different from paper

Issue - State: closed - Opened by kohr-h about 6 years ago - 8 comments

#10 - Any reason for a flip in y

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

#9 - Asynchronous background loading of MRC files

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

#8 - AttributeError: NoneType object has no attribute Mrc

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

#7 - Mach stamp for little endian?

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

#6 - What is the license of the official spec?

Issue - State: closed - Opened by KOLANICH over 6 years ago - 9 comments

#5 - Errors when running against numpy 1.14

Issue - State: closed - Opened by colinpalmer almost 7 years ago - 1 comment

#4 - MRC load problem

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

#3 - it'd be handy to have validator available from the command line

Issue - State: closed - Opened by wojdyr almost 7 years ago - 1 comment

#2 - Fei extended headers

Pull Request - State: closed - Opened by kevinpetersavage about 7 years ago

#1 - Creating large mrcfile with memmap

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