Compatibility with cryoSPARC v4.4.1

scipion-em · Jan 25, 2024 · 5ed4f86 · 5ed4f86
1 parent 0316992
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diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,4 +1,6 @@
 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

diff --git a/README.rst b/README.rst
@@ -34,6 +34,7 @@ You will need to use `3.0.0 <https://scipion-em.github.io/docs/release-3.0.0/doc
 
 **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

diff --git a/cryosparc2/__init__.py b/cryosparc2/__init__.py
@@ -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):

diff --git a/cryosparc2/constants.py b/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()

diff --git a/cryosparc2/protocols/protocol_cryosparc_3D_flex_data_prepare.py b/cryosparc2/protocols/protocol_cryosparc_3D_flex_data_prepare.py
@@ -43,7 +43,7 @@ class ProtCryoSparc3DFlexDataPrepare(ProtCryosparcBase):
     _label = '3D flex data prepare'
     _devStatus = BETA
     _protCompatibility = [V4_1_0, V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1,
-                          V4_4_0]
+                          V4_4_0, V4_4_1]
 
     # --------------------------- DEFINE param functions ----------------------
     def _defineFileNames(self):

diff --git a/cryosparc2/protocols/protocol_cryosparc_3D_flex_mesh_prepare.py b/cryosparc2/protocols/protocol_cryosparc_3D_flex_mesh_prepare.py
@@ -43,7 +43,7 @@ class ProtCryoSparc3DFlexMeshPrepare(ProtCryosparcBase):
     _label = '3D flex mesh prepare'
     _devStatus = BETA
     _protCompatibility = [V4_1_0, V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1,
-                          V4_4_0]
+                          V4_4_0, V4_4_1]
 
     # --------------------------- DEFINE param functions ----------------------
     def _defineFileNames(self):

diff --git a/cryosparc2/protocols/protocol_cryosparc_3D_flex_reconstruction.py b/cryosparc2/protocols/protocol_cryosparc_3D_flex_reconstruction.py
@@ -42,7 +42,7 @@ class ProtCryoSparc3DFlexReconstruction(ProtCryosparcBase):
     """
     _label = '3D flex reconstruction'
     _devStatus = BETA
-    _protCompatibility = [V4_1_0, V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1, V4_4_0]
+    _protCompatibility = [V4_1_0, V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1, V4_4_0, V4_4_1]
 
     # --------------------------- DEFINE param functions ----------------------
     def _defineFileNames(self):

diff --git a/cryosparc2/protocols/protocol_cryosparc_3D_flex_training.py b/cryosparc2/protocols/protocol_cryosparc_3D_flex_training.py
@@ -44,7 +44,7 @@ class ProtCryoSparc3DFlexTraining(ProtCryosparcBase):
     """
     _label = '3D flex training'
     _devStatus = BETA
-    _protCompatibility = [V4_1_0, V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1, V4_4_0]
+    _protCompatibility = [V4_1_0, V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1, V4_4_0, V4_4_1]
 
     # --------------------------- DEFINE param functions ----------------------
     def _defineFileNames(self):

diff --git a/cryosparc2/protocols/protocol_cryosparc_3d_variability_display.py b/cryosparc2/protocols/protocol_cryosparc_3d_variability_display.py
@@ -25,12 +25,11 @@
 # *
 # **************************************************************************
 import os.path
-import zipfile
 
 from pwem.objects import Volume, SetOfVolumes
 from pyworkflow import BETA
 from pyworkflow.protocol.params import (PointerParam, FloatParam,
-                                        LEVEL_ADVANCED, EnumParam, IntParam,
+                                        LEVEL_ADVANCED, EnumParam,
                                         Positive, BooleanParam, StringParam)
 from pwem.protocols import ProtRefine3D
 

diff --git a/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py b/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py
@@ -57,7 +57,7 @@ class ProtCryoSparcGlobalCtfRefinement(ProtCryosparcBase, pwprot.ProtParticles):
     _label = 'global ctf refinement'
     _className = "ctf_refine_global"
     _protCompatibility = [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]
     newParamsName = []
 
     def _initialize(self):

diff --git a/cryosparc2/protocols/protocol_cryosparc_helical_refinement.py b/cryosparc2/protocols/protocol_cryosparc_helical_refinement.py
@@ -54,7 +54,7 @@ class ProtCryoSparcHelicalRefine3D(ProtCryoSparc3DHomogeneousRefine):
     _label = '3D helical refinement'
     _fscColumns = 4
     _protCompatibility = [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_0, V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1, V4_4_0, V4_4_1]
     _className = "helix_refine"
 
     def _defineParams(self, form):
@@ -241,26 +241,20 @@ def processStep(self):
     def _validate(self):
         validateMsgs = cryosparcValidate()
         if not validateMsgs:
-            csVersion = getCryosparcVersion()
-            if [version for version in self._protCompatibility
-                if parse_version(version) >= parse_version(csVersion)]:
-                validateMsgs = gpusValidate(self.getGpuList(), checkSingleGPU=True)
-                if not validateMsgs:
-                    if self.referenceVolume.get() is None and not self.use_cylindrical_model.get():
-                        validateMsgs.append("Cannot generate initial model "
-                                            "without in-plane rotation "
-                                            "information. Please input an "
-                                            "initial model from a previous ab-initio or "
-                                            "refinement protocol, or activate the "
-                                            "'Generate a cylindrical initial "
-                                            "model?' parameter")
-
-                    if self.use_cylindrical_model.get() and self.filament_outer_diameter.get() is None:
-                        validateMsgs.append("Must set the filament outer diameter to use a cylindrical model")
-
-            else:
-                validateMsgs.append("The protocol is not compatible with the "
-                                    "cryoSPARC version %s" % csVersion)
+            validateMsgs = gpusValidate(self.getGpuList(), checkSingleGPU=True)
+            if not validateMsgs:
+                if self.referenceVolume.get() is None and not self.use_cylindrical_model.get():
+                    validateMsgs.append("Cannot generate initial model "
+                                        "without in-plane rotation "
+                                        "information. Please input an "
+                                        "initial model from a previous ab-initio or "
+                                        "refinement protocol, or activate the "
+                                        "'Generate a cylindrical initial "
+                                        "model?' parameter")
+
+                if self.use_cylindrical_model.get() and self.filament_outer_diameter.get() is None:
+                    validateMsgs.append("Must set the filament outer diameter to use a cylindrical model")
+
         return validateMsgs
 
     def _defineParamsName(self):

diff --git a/cryosparc2/protocols/protocol_cryosparc_homogeneous_reconstruction.py b/cryosparc2/protocols/protocol_cryosparc_homogeneous_reconstruction.py
@@ -59,7 +59,7 @@ class ProtCryoSparcHomogeneousReconstruct(ProtCryosparcBase):
     _fscColumns = 6
     _protCompatibility = [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_3_1, V4_4_0, V4_4_1]
     ewsParamsName = []
 
     def _initialize(self):
@@ -355,10 +355,8 @@ def _validate(self):
         validateMsgs = cryosparcValidate()
         if not validateMsgs:
             csVersion = getCryosparcVersion()
-            if [version for version in self._protCompatibility
-                if parse_version(version) >= parse_version(csVersion)]:
-                validateMsgs = gpusValidate(self.getGpuList(),
-                                            checkSingleGPU=True)
+            if [version for version in self._protCompatibility if parse_version(version) <= parse_version(csVersion)]:
+                validateMsgs = gpusValidate(self.getGpuList(), checkSingleGPU=True)
                 if not validateMsgs:
                     particles = self._getInputParticles()
                     if not particles.hasCTF():

diff --git a/cryosparc2/protocols/protocol_cryosparc_homogeneous_refine.py b/cryosparc2/protocols/protocol_cryosparc_homogeneous_refine.py
@@ -60,7 +60,7 @@ class ProtCryoSparc3DHomogeneousRefine(ProtCryosparcBase):
     _className = "homo_refine_new"
     ewsParamsName = []
     _protCompatibility = [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]
 
     # --------------------------- DEFINE param functions ----------------------
     def _defineFileNames(self):
@@ -509,8 +509,7 @@ def _validate(self):
         validateMsgs = cryosparcValidate()
         if not validateMsgs:
             csVersion = getCryosparcVersion()
-            if [version for version in self._protCompatibility
-                if parse_version(version) >= parse_version(csVersion)]:
+            if [version for version in self._protCompatibility if parse_version(version) <= parse_version(csVersion)]:
                 validateMsgs = gpusValidate(self.getGpuList())
                 if not validateMsgs:
                     particles = self._getInputParticles()

diff --git a/cryosparc2/protocols/protocol_cryosparc_new_3D_classification.py b/cryosparc2/protocols/protocol_cryosparc_new_3D_classification.py
@@ -61,7 +61,7 @@ class ProtCryoSparcNew3DClassification(ProtCryosparcBase):
     _label = '3D Classification'
     _className = "class_3D"
     _protCompatibility = [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_0, V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1, V4_4_0, V4_4_1]
 
     def _initialize(self):
         self._defineFileNames()
@@ -486,8 +486,7 @@ def _validate(self):
         validateMsgs = cryosparcValidate()
         if not validateMsgs:
             csVersion = getCryosparcVersion()
-            if [version for version in self._protCompatibility
-                if parse_version(version) >= parse_version(csVersion)]:
+            if [version for version in self._protCompatibility if parse_version(version) <= parse_version(csVersion)]:
                 validateMsgs = gpusValidate(self.getGpuList(),
                                             checkSingleGPU=True)
                 if not validateMsgs:

diff --git a/cryosparc2/protocols/protocol_cryosparc_new_local_refine.py b/cryosparc2/protocols/protocol_cryosparc_new_local_refine.py
@@ -57,7 +57,7 @@ class ProtCryoSparcLocalRefine(ProtCryosparcBase, ProtOperateParticles):
         """
     _label = 'local refinement'
     _protCompatibility = [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_0, V4_1_1, V4_1_2, V4_2_0, V4_2_1, V4_3_1, V4_4_0, V4_4_1]
     _className = "new_local_refine"
     _fscColumns = 6
 
@@ -279,7 +279,7 @@ def _validate(self):
         if not validateMsgs:
             csVersion = getCryosparcVersion()
             if [version for version in self._protCompatibility
-                if parse_version(version) >= parse_version(csVersion)]:
+                if parse_version(version) <= parse_version(csVersion)]:
                 validateMsgs = gpusValidate(self.getGpuList(),
                                             checkSingleGPU=True)
                 if not validateMsgs: