Scipion-em-tomo

Users:
- Add a protocol for filtering coordinates based on a mask.
- TS viewer: Adding angles and the transformation matrix information
- Update napari to v0.4.19
- Steps more precise in GPU usage. Improved execution
Developers:
- Execution mode at class level
- Protocol assign transformation to TS: fix a bug in the assignment of the tilt angle to each new tilt image.

Users:
- Import tomograms, CTFs and Transformation matrices (IMOD): added import functionality using the pattern {TS} to
select the substring that will be considered as tsId.
- Import TS:
* Fix the heterogeneous set of TS validation using a range of angles.
* Multiple TS can be imported without the label {TS}.
- Join heterogeneous sets are possible for tomography objects TS and tomograms.
- New protocol correct tilt offset: It allows to correct the tilt offset of a tilt series
- Fix the protocol tomograms to micrographs. Helps enhanced. ImageHandler replaced by mrcfile.
- Import from Mdoc: more precise error when calculating the dose. GUI log with more information.
- TS viewer: Deleting excluded views and creating a new TS stack.
- Fixing an error creating new outputs through the tiltserie viewer and import error in absence of metadataviewer.
- Fixing an error plotting the defocus values in the ctfEstimation viewer
- Import TS with mdoc: fix in the assignment of the initial dose.
- Assign Transformation Matrix: combine alignments removed. Some fixes at metadata level.
Developers:
- Attribute _acquisition is initialized as None in TSBase, so the coppyAttributes callen in protocol for joining.
sets work properly. The same whith the attribute _origin.
- Method hasAcquisition re-defined in TSBase for the same reason exposed in the previous line.
- Attribute _isHetereogeneous and accessors added to SetOfTomograms and SetOfTiltSeries. Used in the string
representation of both objects.
- TiltSeries: method reStack added and applyTransforma refactored. Both related to the management of the excluded
views.
- Fix update method in Set of Tomos and Set of TS: It does not turn homogeneous sets into heterogeneous ones, nor
does it look at the X and Y dimensions because they are considered heterogeneous under the criteria used before.
Only the third dimension is checked for the heterogeneous set check.
- CTFTomoSeries: method setNumberOfEstimationsInRangeFromDefocusList can handle now the excluded views.
- TCL:
* Attribute _isHetereogeneous checked in the corresponding sets.
* Method checktomograms now is able to check the acquisition.
* Method checkTsOriginMatrix added.
- TS viewer:
* Fix the list of tilt-series viewers
* Using ScipionImageReader to read tiltseries

Users:
- Handling the matching in the ctf import(generalizing without the need to set patterns such as {TS}).
- Refactoring the tiltserie viewer
- Import TS, TSM and tomos: remove double underscore from both the linked filenames and the tsIds.
- Import TS: add a validation for the case of heterogeneous sets of TS in the number of tilt images and providing the
angular data using a range. The cases avoided with this validation prevents erratic behavior in the subsequent
protocols.
Developers:
- Add to Tomogram and SetOfTomograms the attribute _ctfcorrected, the same way it was added to the tilt-series.
- Update the TCL based on the previous point.
v3.7.1: HOTFIX - join TS bug solved (Thanks to Doulin Sheperd).

Developers:
- Add acquistion order attribute to the CTFTomo to provide a robust matching between tilt-images and CTFTomos.
- Add method getTsIds to SetOfTomograms (useful when importing coordinates).
- CTFTomoSeries: add method getCtfTomoFromTi.
- CTFTomo: add acqOrder to the attributes list used on its copy method.
- TiltSeriesBase - method generateTltFile expanded: optional input presentAcqOrders to manage the view exclusion.
- Utils - add method getCommonTsAndCtfElements to intersect tilt images and CTFs based on the value of the
attribute acquisition order, or index in case it's not present or empty (backwards compatibility)
- SetOfCTFTomoSeries: add method getTSIds, just the same as for SetOfTiltSeries and SetOfCoordinates3D.
- Method getTSIds methods simplified. They call now getUniqueValues instead of aggregate.

Users:
- Collapse the tilt-series tree by default in the tomo data viewer
- Fix in protocol import TS: when providing mdoc files, label DividedBy2 is now only applied in the case of
calculating it from fields MinMaxMean, PixelSpacing and CountsPerElectron (case 4).

Developers:
- Fix: class Tomogram method getDim removed as it did not manage heterogeneous sets correctly when iterating (read the
header once, stored it and reused). The Volume method is used now instead, as it reads the size from the file
header for each file.
- use setFramesFrange when importing TS movies
- Class Tomogram method getDim removed as it did not manage heterogeneous sets correctly when iterating (read the
header once, stored it and reused). The Volume method is used now instead, as it reads the size from the file
header for each file.

Users:
- Tilt series subsets and CTFTomoseries clone the enable flag
- Acquisition data storage fixed when importing tilt series and tilt series movies (min angle, max angle, and step)

Developers:
- Test dataset relion40_sta_tutorial_data expanded.
- TCL: methods dor checking sets of TS and TsM improved.