I2PC / xmippCore

Core functions for Xmipp and sharing with other packages (like Scipion)
GNU General Public License v3.0
4 stars 2 forks source link

Transposing volume axes for modified volume headers #178

Closed MartinSalinas98 closed 1 year ago

MartinSalinas98 commented 1 year ago

Xmipp, until now, did not read volume headers, and assumed a certain order was followed (fields mapc-mapr-maps always were 1,2,3).

This caused some volumes with modified order to not be processed properly within xmipp, being unintentionally transposed.

With this PR, Xmipp will now be able to read any volume with any values of those fields correctly.

PS: Updated action versions & Ubuntu version.

MartinSalinas98 commented 1 year ago

Update: Converted MRC is slightly smaller in test. Apparently Xmipp does not (and has not done for a long time) properly write the metadata for pixel size. image This image is original & converted volumes, with full contour level in Chimera to visualize the size of the full cube they are in. It is appreciable that the converted (yellow) is somewhat smaller.

Without taking that into account, conversion works as expected with the changes in mapc,mapr,maps header values.

sonarcloud[bot] commented 1 year ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

warning The version of Java (11.0.3) you have used to run this analysis is deprecated and we will stop accepting it soon. Please update to at least Java 17. Read more here