Merge pull request #155 from scipion-em/devel

Compatibility with cryoSPARC v4.4.1

CHANGES.txt

@@ -1,3 +1,12 @@
+Dec 22, 2023    - **v4.0.10**
+                Compatibility with cryoSPARC v4.4.1
+
+                Add new protocols:
+                 * **3D Variability Analysis**: Protocol to compute the principle modes of variability with a dataset of aligned particles
+                 * **3D Variability Display**: Protocol to create various versions of a 3D variability result that can be used for display
+                 * **Blob Picker**: Automatically picks particles by searching for Gaussian signals.
+                 * **Patch CTF Estimation**: Patch-based CTF estimation automatically estimates defocus variation for tilted, bent, deformed samples and is accurate for all particle sizes and types including flexible and membrane proteins.
+
 Nov 17, 2023    - **v4.0.9**
                  Compatibility with cryoSPARC v4.4.0
                  Handling aborted protocols/jobs

README.rst

@@ -24,26 +24,31 @@ You will need to use `3.0.0 <https://scipion-em.github.io/docs/release-3.0.0/doc
 * **Symmetry Expansion**: Duplicate particles around a point-group symmetry.
 * **Homogeneous Reconstruction**: Reconstruct half-maps from input particles with alignments
 * **3D Classification**: Classify particles into multiple 3D classes and optimize 3D class densities (currently, without re-aligning particle pose or shift).
+* **3D Variability Analysis**: Protocol to compute the principle modes of variability with a dataset of aligned particles
+* **3D Variability Display**: Protocol to create various versions of a 3D variability result that can be used for display
+* **Blob Picker**: Automatically picks particles by searching for Gaussian signals.
+* **Patch CTF Estimation**:  Patch-based CTF estimation automatically estimates defocus variation for tilted, bent, deformed samples and is accurate for all particle sizes and types including flexible and membrane proteins.
 
 **Latest plugin version**
 ==========================
 
+**v4.0.10**
+-----------
+* **new**        Compatibility with cryoSPARC v4.4.1
+* **new**        Add new protocols:
+
+                 * **3D Variability Analysis**: Protocol to compute the principle modes of variability with a dataset of aligned particles
+                 * **3D Variability Display**: Protocol to create various versions of a 3D variability result that can be used for display
+                 * **Blob Picker**: Automatically picks particles by searching for Gaussian signals.
+
+
+
+
 **v4.0.9**
 -----------
 * **new**        Compatibility with cryoSPARC v4.4.0
 * **fixed**      Handling aborted protocols/jobs
 
-**v4.0.8**
------------
-* **new**        Compatibility with cryoSPARC v4.3.1
-* **removed**    Deprecated protocols removed: Legacy Refine, Legacy no uniform refine, Legacy naive local refine.
-
-**v4.0.7**
------------
-* **new**     :  Compatibility with cryoSPARC v4.2.1
-* **new**        Plugin operation in a cluster
-* **fixed**      Fixed an installation error
-* **fixed**      Fixed an error related with the calculation of the particles shifts
 
 **Installing the plugin**
 =========================

cryosparc2/__init__.py

@@ -31,7 +31,7 @@
 
 from .constants import *
 
-__version__ = '4.0.9'
+__version__ = '4.0.10'
 _references = ['Punjani2017', 'Brubaker2017', 'daniel_asarnow_2019_3576630']
 _logo = 'cryosparc2_logo.png'
 
@@ -42,7 +42,7 @@ class Plugin(em.Plugin):
     _pathVars = [CRYOSPARC_HOME]
     _supportedVersions = [V3_0_0, V3_0_1, V3_1_0, V3_2_0, V3_3_0, V3_3_1,
                           V3_3_2, V4_0_0, V4_0_1, V4_0_2, V4_0_3, V4_1_0,
-                          V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1, V4_4_0]
+                          V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1, V4_4_0, V4_4_1]
 
     @classmethod
     def _defineVariables(cls):

cryosparc2/constants.py

@@ -75,6 +75,7 @@ def getPyemEnvName(version):
 V4_2_1 = 'V4.2.1'
 V4_3_1 = 'V4.3.1'
 V4_4_0 = 'V4.4.0'
+V4_4_1 = 'V4.4.1'
 
 # Symmetry dict
 CS_SYM_NAME = dict()
@@ -125,9 +126,9 @@ def getPyemEnvName(version):
 ANGDIST_CHIMERA = 1
 
 # VOLUME_SLICES = 0
-VOLUME_CHIMERA = 1
+VOLUME_CHIMERA = 0
 VOLUME_CRYOSPARC = 0
-DATA_VIEWER = 0
+DATA_VIEWER = 1
 
 fscValues = dict()
 fscValues['fsc_nomask'] = 'No mask'

cryosparc2/protocols/__init__.py

@@ -39,11 +39,18 @@
 from .protocol_cryosparc_symmetry_expansion import ProtCryoSparcSymmetryExpansion
 from .protocol_cryosparc_homogeneous_reconstruction import ProtCryoSparcHomogeneousReconstruct
 from .protocol_cryosparc_new_3D_classification import ProtCryoSparcNew3DClassification
-"""
+
 from .protocol_cryosparc_3d_variability import ProtCryoSparc3DVariability
-from .protocol_cryosparc_3d_variability_display import ProtCryoSparc3DVariabilityAnalisys
+from .protocol_cryosparc_3d_variability_display import ProtCryoSparc3DVariabilityDisplay
+
+from .protocol_cryosparc_blob_picker import ProtCryoSparcBlobPicker
+from .protocol_cryosparc_patch_ctf_estimation import ProtCryoSparcPatchCTFEstimate
 
+"""
 from .protocol_cryosparc_3D_flex_data_prepare import ProtCryoSparc3DFlexDataPrepare
+from .protocol_cryosparc_3D_flex_mesh_prepare import ProtCryoSparc3DFlexMeshPrepare
 from .protocol_cryosparc_3D_flex_training import ProtCryoSparc3DFlexTraining
 from .protocol_cryosparc_3D_flex_reconstruction import ProtCryoSparc3DFlexReconstruction
 """
+
+

cryosparc2/protocols/protocol_base.py

@@ -45,7 +45,7 @@
                      doImportParticlesStar, doImportVolumes, killJob, clearJob,
                      get_job_streamlog, getSystemInfo, getJobStatus,
                      STOP_STATUSES, getCryosparcVersion, getProjectInformation,
-                     getCryosparcProjectId, _getLicenceFromFile)
+                     getCryosparcProjectId, _getLicenceFromFile, doImportMicrographs)
 
 
 class ProtCryosparcBase(pw.EMProtocol):
@@ -118,6 +118,11 @@ def convertInputStep(self):
             self._importMask()
         else:
             self.mask = pwobj.String()
+
+        micrographs = self._getInputMicrographs()
+        if micrographs is not None:
+            self._importMicrographs()
+
         self._store(self)
 
     def _getScaledAveragesFile(self, csAveragesFile, force=False):
@@ -187,9 +192,14 @@ def _getInputMask(self):
             return self.refMask.get()
         return None
 
+    def _getInputMicrographs(self):
+        if self.hasAttribute('inputMicrographs'):
+            return self.inputMicrographs.get()
+        return None
+
     def _initializeVolumeSuffix(self):
         """
-        Create a output volume suffix depend of the CS version
+        Create an output volume suffix depend on the CS version
         """
         cryosparcVersion = parse_version(getCryosparcVersion())
         self.outputVolumeSuffix = '.imported_volume.map'
@@ -243,13 +253,19 @@ def _importMask(self):
         self.mask = pwobj.String(str(importMaskJob.get()) + self.outputMaskSuffix)
 
     def _importParticles(self):
-
         # import_particles_star
         importedParticlesJob = doImportParticlesStar(self)
         self.currenJob = pwobj.String(str(importedParticlesJob.get()))
         self.particles = pwobj.String(str(importedParticlesJob.get()) +
                                       '.imported_particles')
 
+    def _importMicrographs(self):
+        importedMicrographsJob = doImportMicrographs(self)
+        self.currenJob = pwobj.String(str(importedMicrographsJob.get()))
+        self.micrographs = pwobj.String(str(importedMicrographsJob.get()) +
+                                      '.imported_micrographs')
+
+
     def setAborted(self):
         """ Set the status to aborted and updated the endTime. """
         pw.EMProtocol.setAborted(self)