Merge pull request #194 from I2PC/release-3.24.06

Release 3.24.06

.github/workflows/buildPlugin.yml

@@ -11,25 +11,29 @@ jobs:
   build:
     # Specify the machine to run the job on
     runs-on: ubuntu-22.04
-
+
+    # Avoid send statistics 
+    env:
+      SEND_INSTALLATION_STATISTICS: "False"
+
     # Define the steps to be taken in the job
-    steps:    
-    # Installing dependencies
+    steps:
+    - name: Free Disk Space (Ubuntu only)
+      uses: jlumbroso/free-disk-space@main
+
     - name: Install dependencies 
       run: |
         sudo apt-get update
         sudo apt-get install -y libfftw3-dev libopenmpi-dev openmpi-bin libhdf5-dev python3-numpy python3-dev libtiff5-dev unzip libsqlite3-dev default-jdk git cmake libopencv-dev libopenmpi-dev make cmake
     
-    # Installing CUDA
     - name: Install CUDA
-      uses: Jimver/cuda-toolkit@v0.2.11
+      uses: Jimver/cuda-toolkit@master
       id: cuda-toolkit
       with:
         cuda: '11.8.0'
         method: network
         sub-packages: '["nvcc", "toolkit"]'
 
-    # Installing Miniconda
     - name: Install Miniconda
       working-directory: ${{ github.workspace }}/../
       run: |
@@ -38,7 +42,6 @@ jobs:
         source ./miniconda/etc/profile.d/conda.sh
         conda update -n base -c defaults conda -y
         
-    # Installing Scipion
     - name: Install Scipion
       working-directory: ${{ github.workspace }}/../
       run: |
@@ -53,7 +56,6 @@ jobs:
         conda activate scipion3
         pip install scons
         
-    # Cloning Xmipp 
     - name: Cloning Xmipp
       working-directory: ${{ github.workspace }}/../
       run: git clone https://github.com/I2PC/xmipp.git
@@ -98,13 +100,20 @@ jobs:
 
     # Check out the repository in the pull request
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@main
       with:
         ref: ${{ github.head_ref }}
-
-    # Install plugin from the pull request using the Scipion3 installp command
+
     - name: Install plugin from pull request
       working-directory: ${{ github.workspace }}
+      run: ../scipion/scipion3 installp -p . --devel
+
+    # Currently, test script is being downloaded from scipion-chem, but that should be temporary
+    # Ideally, the script might be included in scipion core to be able to import it,
+    # or maybe host it in a separate repository common with useful scripts for all scipion plugins
+    - name: Run tests
+      working-directory: ${{ github.workspace }}/${{ vars.FOLDER_WITH_VERSION }}
       run: |
-        # Install the repository from the pull request
-        ../scipion/scipion3 installp -p . --devel
+        wget https://raw.githubusercontent.com/scipion-chem/scipion-chem/devel/pwchem/runTests.py
+        eval "$(${{ github.workspace }}/../miniconda/bin/conda shell.bash hook)"
+        python runTests.py ${{ github.workspace }}/../scipion/scipion3 ${{ vars.FOLDER_WITH_VERSION }} -noGPU -testData=testData.json -j=3

.gitignore

@@ -4,6 +4,7 @@
 .pydevproject
 .classpath
 .idea
+.vscode
 
 #### Python
 build/

CHANGES.md

@@ -1,3 +1,17 @@
+## V3.24.06
+   - New protocols:
+      - apply_segmentation: Applies a segmentation to a set of tomograms.
+      - segment_morphology: Segments a tomogram by means of thresholding, different kind of filters and morphological operations.
+   - Protocols updated
+      - deep_misalignment: updated model, minor improvements
+      - extract_subtomos: improve extract subtomos readability
+   - Protocols fixed
+      - dose_filter: Dose filter, removing extract stacks
+   - More xmippTomo
+      - New xmippBase repository to manage shared protocols with Xmipp
+      - protocols deprecated: score_transform, denoising_confidence
+      - Removed tilt particles object (not used)
+
 ## V3.23.11
    - Protocols updated
       - applyAlignmentTS

requirements.txt

@@ -1,3 +1,4 @@
 scipion-em-xmipp
 scipion-em-tomo
-scipion-em >= 3.0.8
+scipion-em >= 3.0.8
+scipion-em-xmippBase

xmipptomo/__init__.py

@@ -29,7 +29,7 @@
 
 _logo = "xmipp_logo.png"
 _references = ['delaRosaTrevin2013', 'Jimenez2022']
-__version__ = "3.23.11.0" #X.YY.MM.sv
+__version__ = "3.24.06.0" #X.YY.MM.sv
         # X.Y.M = version of the xmipp release associated.
         # sv = Set this to ".0" on each xmipp  release.
         # For not release version (hotfix) increase it --> ".1", ".2", ...

xmipptomo/legacy/tests/test_protocol_score_transform.py

@@ -0,0 +1,71 @@
+# **************************************************************************
+# *
+# * Authors:    Federico P. de Isidro-Gomez
+# *
+# * [1] Centro Nacional de Biotecnologia, CSIC, Spain
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 2 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address 'scipion@cnb.csic.es'
+# *
+# **************************************************************************
+import numpy as np
+from pyworkflow.tests import BaseTest, setupTestProject
+from tomo.tests import DataSet
+
+from xmipptomo.protocols import XmippProtScoreTransform
+from tomo.protocols import ProtImportSubTomograms
+
+class TestXmippTomoScoreTransform(BaseTest):
+    """This class check if the protocol score_transform works properly."""
+
+    @classmethod
+    def setUpClass(cls):
+        setupTestProject(cls)
+        cls.dataset = DataSet.getDataSet('tomo-em')
+        cls.setOfSubtomograms = cls.dataset.getFile('basename.hdf')
+
+    def _runImportSubtomos(self, label):
+        protImport = self.newProtocol(ProtImportSubTomograms,
+                                      filesPath=self.setOfSubtomograms,
+                                      samplingRate=5,
+                                      label=label)
+        self.launchProtocol(protImport)
+        self.assertIsNotNone(protImport.outputSubTomograms,
+                             "There was a problem with import subtomograms output")
+        return protImport.outputSubTomograms
+
+    def _scoreTransformations(self, firstSubtomos, secondSubtomos):
+        scoredTr = self.newProtocol(XmippProtScoreTransform,
+                                   firstSubtomos=firstSubtomos,
+                                   secondSubtomos=secondSubtomos,
+                                   label='Score Subtomogram Transformations')
+        self.launchProtocol(scoredTr)
+        self.assertIsNotNone(scoredTr.outputSetOfSubtomogram,
+                             "There was a problem with score subtomograms output")
+        return scoredTr.outputSetOfSubtomogram
+
+    def test_scoreTransformations(self):
+        firstSubtomos = self._runImportSubtomos('First Subtomograms')
+        secondSubtomos = self._runImportSubtomos('Second Subtomograms')
+        scoredSubtomos = self._scoreTransformations(firstSubtomos, secondSubtomos)
+        self.assertTrue(scoredSubtomos.getSize() == 4)
+        dist = scoredSubtomos.aggregate(["MAX"], "distanceScore", ["distanceScore"])
+        dist = np.asarray([d["distanceScore"] for d in dist])
+        meanDist = np.mean(dist)
+        self.assertTrue(meanDist == 0)
+        return scoredSubtomos

xmipptomo/protocols/__init__.py

@@ -35,8 +35,6 @@
 from .protocol_dose_filter import XmippProtDoseFilter
 from .protocol_filter_coordinates_by_map import XmippProtFilterCoordinatesByMap
 from .protocol_crop_tomograms import XmippProtCropTomograms
-from .protocol_denoising_confidence import XmippProtConfTomo
-from .protocol_extract_particlestacks import XmippProtExtractParticleStacks
 from .protocol_extract_subtomos import XmippProtExtractSubtomos
 from .protocol_flexalign import XmippProtTsFlexAlign
 from .protocol_peak_high_contrast import XmippProtPeakHighContrast
@@ -49,9 +47,10 @@
 from .protocol_resolution_local_monotomo import XmippProtMonoTomo
 from .protocol_roiIJ import XmippProtRoiIJ
 from .protocol_score_coordinates import XmippProtScoreCoordinates
-from .protocol_score_transform import XmippProtScoreTransform
 from .protocol_splitTS import XmippProtSplitTiltSeries
 from .protocol_subtraction_subtomo import XmippProtSubtractionSubtomo
 from .protocol_subtomo_map_back import XmippProtSubtomoMapBack
 from .protocol_half_maps_subtomos import XmippProtHalfMapsSubtomo
 from .protocol_project_subtomograms import XmippProtProjectSubtomograms
+from .protocol_apply_segmentation import XmippProtApplySegmentation
+from .protocol_segment_morphology import XmippProtMorphology