scipion-em-xmipp 26.0.2__tar.gz → 26.2.0__tar.gz

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/CHANGELOG.md

@@ -1,3 +1,19 @@
+## Release 26.2.0
+- More scipion-em-xmipp
+   - xmipp3-installer package installed from pypi, reverting previous temporal fix
+   - Added new dependencie to solve error with libicu18
+ 
+- Protocols deprecated (For more details visit [this](https://github.com/I2PC/xmipp/wiki/Deprecating-programs-and-protocols](https://i2pc.github.io/docs/Utils/Deprecated-programs/index.html)))
+   - DeepCenter
+  
+## Release 26.1.0
+- Protocols updated
+  - deep_micrograph_cleaner: Showing thumbnails of micrographs with the mask and the coordinates stamps
+  - protocol_extract_particles, protocol_preprocess, protocol_compute_likelihood, protocol_extract_particles_pairs: fix typo
+
+- More scipion-em-xmipp
+   - xmipp3-installer package installed from github release and not from pypi
+
 ## Release 26.0.2
 - More scipion-em-xmipp
    - Remove scipion dependencies from requirements   

{scipion_em_xmipp-26.0.2/scipion_em_xmipp.egg-info → scipion_em_xmipp-26.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scipion-em-xmipp
-Version: 26.0.2
+Version: 26.2.0
 Summary: Plugin to use Xmipp programs within the Scipion framework.
 Author-email: Oier Lauzirika Zarrabeitia <oierlauzi@bizkaia.eu>, Alberto Garcia Mena <alberto.garcia@cnb.csic.es>, Carlos Oscar Sanchez Sorzano <coss@cnb.csic.es>
 License: GNU General Public License v3 (GPLv3)
@@ -17,7 +17,7 @@ Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter
 Requires-Dist: PyWavelets
-Requires-Dist: xmipp3-installer==2.*
+Requires-Dist: xmipp3-installer<3.0.0,>=2.0.4
 Requires-Dist: numpy==1.*
 Dynamic: license-file
 

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/requirements.txt

@@ -5,5 +5,5 @@ joblib
 peppercorn
 plotter
 PyWavelets
-xmipp3-installer==2.*
+xmipp3-installer>=2.0.4,<3.0.0
 numpy==1.*

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0/scipion_em_xmipp.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scipion-em-xmipp
-Version: 26.0.2
+Version: 26.2.0
 Summary: Plugin to use Xmipp programs within the Scipion framework.
 Author-email: Oier Lauzirika Zarrabeitia <oierlauzi@bizkaia.eu>, Alberto Garcia Mena <alberto.garcia@cnb.csic.es>, Carlos Oscar Sanchez Sorzano <coss@cnb.csic.es>
 License: GNU General Public License v3 (GPLv3)
@@ -17,7 +17,7 @@ Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter
 Requires-Dist: PyWavelets
-Requires-Dist: xmipp3-installer==2.*
+Requires-Dist: xmipp3-installer<3.0.0,>=2.0.4
 Requires-Dist: numpy==1.*
 Dynamic: license-file
 

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/scipion_em_xmipp.egg-info/SOURCES.txt

@@ -37,6 +37,8 @@ xmipp3/legacy/protocols/protocol_classification_gpuCorr_full.py
 xmipp3/legacy/protocols/protocol_classification_gpuCorr_semi.py
 xmipp3/legacy/protocols/protocol_classify_kmeans2d.py
 xmipp3/legacy/protocols/protocol_deep_align.py
+xmipp3/legacy/protocols/protocol_deep_center.py
+xmipp3/legacy/protocols/protocol_deep_center_predict.py
 xmipp3/legacy/protocols/protocol_deep_denoising.py
 xmipp3/legacy/protocols/protocol_enrich.py
 xmipp3/legacy/protocols/protocol_extract_particles_movies.py
@@ -104,8 +106,6 @@ xmipp3/protocols/protocol_ctf_correct_phase.py
 xmipp3/protocols/protocol_ctf_correct_wiener2d.py
 xmipp3/protocols/protocol_ctf_defocus_group.py
 xmipp3/protocols/protocol_ctf_micrographs.py
-xmipp3/protocols/protocol_deep_center.py
-xmipp3/protocols/protocol_deep_center_predict.py
 xmipp3/protocols/protocol_deep_hand.py
 xmipp3/protocols/protocol_deep_micrograph_screen.py
 xmipp3/protocols/protocol_denoise_particles.py

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/scipion_em_xmipp.egg-info/requires.txt

@@ -5,5 +5,5 @@ joblib
 peppercorn
 plotter
 PyWavelets
-xmipp3-installer==2.*
+xmipp3-installer<3.0.0,>=2.0.4
 numpy==1.*

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/__init__.py

@@ -35,7 +35,7 @@ import pyworkflow.utils as pwutils
 from scipion.install.funcs import CondaCommandDef
 from .base import *
 from .version import *
-from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME, XMIPP_CUDA_BIN, XMIPP_CUDA_LIB, XMIPP_GIT_URL
+from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME, XMIPP_CUDA_BIN, XMIPP_CUDA_LIB, XMIPP_GIT_URL, XMIPP3_INSTALLER_URL
 
 
 _references = ['delaRosaTrevin2013', 'Sorzano2013', 'Strelak2021']
@@ -47,6 +47,7 @@ type_of_version = version.type_of_version
 _logo = version._logo
 _currentDepVersion = version._currentDepVersion
 __version__ = version.__version__
+_xmipp3_installerV = "v2.0.4"
 
 
 class Plugin(pwem.Plugin):
@@ -126,7 +127,6 @@ class Plugin(pwem.Plugin):
         env.set('MATLABPATH', os.path.join(os.environ[XMIPP_HOME],
                                            'libraries', 'bindings', 'matlab'),
                 pwutils.Environ.BEGIN)
-
         return env
 
     @classmethod
@@ -147,7 +147,7 @@ class Plugin(pwem.Plugin):
             'dist/xmipp.bashrc'
         ]
         
-        # When changing dependencies, increment _currentDepVersion
+        # When changing dependencies, increment 
         CONDA_DEPENDENCIES = [
 	    "'cmake>=3.18,<4'", #cmake-4 is not compatible with Relion compilation
             "hdf5>=1.18",
@@ -160,7 +160,8 @@ class Plugin(pwem.Plugin):
             "libjpeg-turbo",
         ]
 
-        CONDA_LIBSTDCXX_PACKAGE = "libstdcxx-ng"
+        CONDA_LIBSTDCXX_PACKAGE = "libstdcxx-ng "
+        CONDA_ICU_PACKAGE = 'icu=72'
 
         if Config.isCondaInstallation():
             condaEnvPath = os.environ['CONDA_PREFIX']
@@ -168,7 +169,7 @@ class Plugin(pwem.Plugin):
 
             commands = CondaCommandDef(scipionEnv, cls.getCondaActivationCmd())
             #commands.condaInstall('-c conda-forge --yes '  + ' '.join(CONDA_DEPENDENCIES))
-            commands.condaInstall('-c conda-forge --yes '  + CONDA_LIBSTDCXX_PACKAGE)
+            commands.condaInstall('-c conda-forge --yes '  + CONDA_LIBSTDCXX_PACKAGE + CONDA_ICU_PACKAGE)
             commands.touch("deps_installed.txt")
             env.addPackage(
                 'xmippDep', version=_currentDepVersion,
@@ -177,14 +178,12 @@ class Plugin(pwem.Plugin):
                 neededProgs=['conda'],
                 default=True
             )
-        
         if develMode:
             xmippSrc = 'xmippDev'
             installCommands = [
 		        (f'cd {pwem.Config.EM_ROOT} && rm -rf {xmippSrc} && '
 		         f'git clone {XMIPP_GIT_URL} {xmippSrc} && '
 		         f'cd {xmippSrc} && '
-		         #f'git checkout {branchTest} && '
 		         f'./xmipp ', COMPILE_TARGETS)
 	        ]
 
@@ -200,9 +199,9 @@ class Plugin(pwem.Plugin):
             xmippSrc = f'xmipp3-{version._binVersion}'
             installCommands = [
                 (f'cd .. && rm -rf {xmippSrc} && '
-                f'git clone {XMIPP_GIT_URL} -b {version._binVersion} {xmippSrc} && '
-                f'cd {xmippSrc} && '
-                f'./xmipp', COMPILE_TARGETS)
+                 f'git clone {XMIPP_GIT_URL} -b {version._binVersion} {xmippSrc} && '
+                 f'cd {xmippSrc} && '
+                 f'./xmipp', COMPILE_TARGETS)
             ]
             env.addPackage(
 	                'xmipp3', version=version._binVersion,

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/constants.py

@@ -31,6 +31,7 @@ This modules contains constants related to Xmipp3 protocols
 XMIPP_GIT_URL = 'https://github.com/I2PC/xmipp3.git'
 XMIPP_URL = 'https://github.com/i2pc/scipion-em-xmipp'
 XMIPP_HOME = 'XMIPP_HOME'
+XMIPP3_INSTALLER_URL = 'https://github.com/I2PC/xmipp3-installer.git'
 NMA_HOME = 'NMA_HOME'
 XMIPP_DLTK_NAME = 'deepLearningToolkit'  # consider to change it to xmipp_DLTK to make short it
 XMIPP_CUDA_BIN = 'XMIPP_CUDA_BIN'

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/legacy/protocols/protocol_extract_particles_movies.py

@@ -152,7 +152,7 @@ class XmippProtExtractMovieParticles(ProtExtractMovieParticles):
                       help='Pixels outside this circle are assumed to be '
                            'noise and their stddev is set to 1. Radius for '
                            'background circle definition (in pix.). If this '
-                           'value is 0, then half the box size is used.',
+                           'value is less than or equal to 0, then half the box size is used.',
                       expertLevel=LEVEL_ADVANCED)
 
         form.addParallelSection(threads=3, mpi=1)

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/protocols/__init__.py

@@ -133,6 +133,4 @@ from .protocol_volume_consensus import XmippProtVolConsensus
 from .protocol_volume_local_adjust import XmippProtLocalVolAdj
 from .protocol_classes_2d_mapping import XmippProtCL2DMap
 from .protocol_deep_hand import XmippProtDeepHand
-from .protocol_deep_center import XmippProtDeepCenter
 from .protocol_compute_likelihood import XmippProtComputeLikelihood
-from .protocol_deep_center_predict import XmippProtDeepCenterPredict

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/protocols/protocol_compute_likelihood.py

@@ -105,8 +105,8 @@ class XmippProtComputeLikelihood(ProtAnalysis3D):
 
         form.addParam('doNorm', BooleanParam, default=False,
                       label='Normalize', expertLevel=LEVEL_ADVANCED,
-                      help='Whether to subtract background gray values and normalize'
-                           'so that in the background there is 0 mean and'
+                      help='Whether to subtract background gray values and normalize '
+                           'so that in the background there is 0 mean and '
                            'standard deviation 1. This is applied to particles and volumes')
         form.addParam('normType', EnumParam, condition='doNorm',
                       label='Particle normalization type', expertLevel=LEVEL_ADVANCED,

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/protocols/protocol_deep_micrograph_screen.py

@@ -33,12 +33,26 @@ import pyworkflow.protocol.params as params
 from pwem.protocols import ProtExtractParticles
 from pyworkflow.object import Set, Pointer
 
+import mrcfile
+from scipy.ndimage import zoom
+import matplotlib
+from matplotlib.lines import Line2D
+from matplotlib.patches import Patch
+matplotlib.use('Agg')
+from matplotlib.patches import Circle
+from matplotlib.collections import PatchCollection
+
 from xmipp3.base import XmippProtocol
 from xmipp_base import createMetaDataFromPattern
 from xmipp3.convert import (writeMicCoordinates, readSetOfCoordinates)
 from xmipp3.constants import SAME_AS_PICKING, OTHER
 from pyworkflow import BETA, UPDATED, NEW, PROD
+import numpy as np
+import mrcfile
+import matplotlib.pyplot as plt
 
+MAX_SIZE_THUMB=512
+NUM_THUMBNAILS=45
 
 class XmippProtDeepMicrographScreen(ProtExtractParticles, XmippProtocol):
     """Removes coordinates located in carbon regions or large impurities in micrographs using a pre-trained deep learning model. This screening improves particle picking accuracy by filtering out false positives from contaminated areas."""
@@ -113,6 +127,12 @@ class XmippProtDeepMicrographScreen(ProtExtractParticles, XmippProtocol):
         form.addParam("saveMasks", params.BooleanParam, default=False,expertLevel=params.LEVEL_ADVANCED,
                       label="saveMasks", help="Save predicted masks?")
 
+        form.addParam("saveMicThumbnailWithMask", params.BooleanParam, default=True, expertLevel=params.LEVEL_ADVANCED,
+                      condition='saveMasks == True',
+                      label="Save thumbnails (mics and mask)",
+                      help="Save a set of 50 micrographs with the predicted masks stamp and coords stamp")
+
+
         form.addHidden(params.USE_GPU, params.BooleanParam, default=True,
                        label="Use GPU for execution",
                        help="This protocol has both CPU and GPU implementation. "
@@ -148,6 +168,7 @@ class XmippProtDeepMicrographScreen(ProtExtractParticles, XmippProtocol):
         # before the actual processing
         pwutils.makePath(self._getExtraPath('inputCoords'))
         pwutils.makePath(self._getExtraPath('outputCoords'))
+        pwutils.makePath(self._getExtraPath('thumbnails'))
         if self.saveMasks.get():
           pwutils.makePath(self._getExtraPath("predictedMasks"))
         self._setupBasicProperties()
@@ -179,7 +200,6 @@ class XmippProtDeepMicrographScreen(ProtExtractParticles, XmippProtocol):
 
     def extractMicrographListStepOwn(self, micKeyList, *args):
         micList = []
-
         for micName in micKeyList:
             mic = self.micDict[micName]
             micDoneFn = self._getMicDone(mic)
@@ -197,7 +217,12 @@ class XmippProtDeepMicrographScreen(ProtExtractParticles, XmippProtocol):
 
         self._computeMaskForMicrographList(micList, *args)
 
+        thumbnailCounter = 0
         for mic in micList:
+            if self.saveMicThumbnailWithMask.get():
+                if thumbnailCounter <= NUM_THUMBNAILS:
+                    self._generateThumbnail(mic)
+                    thumbnailCounter += 1
             # Mark this mic as finished
             open(self._getMicDone(mic), 'w').close()
 
@@ -524,3 +549,126 @@ class XmippProtDeepMicrographScreen(ProtExtractParticles, XmippProtocol):
         self._defineSourceRelation(inputset,
                                    Pointer(value=self, extended=outputName))
         self._store()
+
+    def _generateThumbnail(self, mic):
+        """
+        Generate a thumbnail PNG for a given micrograph.
+
+        Steps performed:
+        1. Load the micrograph from MRC file and normalize pixel values to 0-255.
+        2. Optionally read particle coordinates from a .pos file.
+        3. Optionally read a predicted mask from a .mrc file.
+        4. Resize the image, mask, and scale coordinates if larger than maxSize.
+        5. Overlay the mask in blue and draw particles as red circles.
+        6. Save the final thumbnail as a PNG with minimal padding and compression.
+
+        Parameters
+        ----------
+        mic : Micrograph object
+            The micrograph to generate the thumbnail for.
+        maxSize : int, optional
+            Maximum size (in pixels) for the thumbnail (default is 512).
+
+        Returns
+        -------
+        None
+            The thumbnail is saved directly to the 'thumbnails' directory.
+        """
+        micFn = mic.getFileName()
+        micBase = pwutils.removeBaseExt(os.path.basename(micFn))
+
+        posFn = self._getExtraPath('outputCoords', micBase + '.pos')
+        maskFn = self._getExtraPath('predictedMasks', micBase + '.mrc')
+        thumbFn = self._getExtraPath('thumbnails', micBase + '.png')
+        if os.path.exists(thumbFn):
+            return
+
+        # --- Read micrograph ---
+        with mrcfile.open(micFn, permissive=True) as mrc:
+            img = mrc.data.astype(np.float32)
+
+        # --- Normalize and convert to uint8 ---
+        p1, p99 = np.percentile(img, (1, 99))
+        img = np.clip((img - p1) / (p99 - p1), 0, 1)
+        img = (img * 255).astype(np.uint8)
+
+        # --- Read coordinates ---
+        if  os.path.exists(posFn):
+            coords = self.read_star_coordinates(posFn)
+
+        # --- Read mask ---
+        mask = None
+        if os.path.exists(maskFn):
+            with mrcfile.open(maskFn, permissive=True) as mrc:
+                mask = mrc.data.astype(np.float32)
+            mask = np.clip(mask, 0.0, 1)
+
+        # --- Resize image, mask, and scale coordinates/radius ---
+        h, w = img.shape
+        scale = max(MAX_SIZE_THUMB / h, MAX_SIZE_THUMB / w)
+
+        if scale < 1.0:
+            # Bilinear resize for image
+            img = zoom(img, (scale, scale), order=1, prefilter=False).astype(np.uint8)
+            # Nearest neighbor resize for mask
+            if mask is not None:
+                mask = zoom(mask, (scale, scale), order=0)
+            # Scale coordinates
+            if coords:
+                coords = [(x * scale, y * scale) for x, y in coords]
+
+        radius = (self.getBoxSize() * scale) / 4
+        h, w = img.shape
+
+        # --- Create figure ---
+        fig, ax = plt.subplots(figsize=(w / 100, h / 100), dpi=100)
+        ax.set_position([0, 0, 1, 1])  # axes fill figure
+        ax.axis('off')
+        # --- Show image ---
+        ax.imshow(img, cmap='gray', origin='upper', vmin=0, vmax=255)
+        # --- Overlay mask in blue ---
+        if mask is not None:
+            ax.imshow(mask, cmap='YlGnBu', origin='upper', alpha=mask)
+
+        # --- Fix axes, remove background and borders ---
+        ax.set_xlim(0, w)
+        ax.set_ylim(h, 0)
+        ax.set_facecolor('none')
+
+        # --- Draw particles using PatchCollection ---
+        if coords:
+            patches = [Circle((x, y), radius=radius) for x, y in coords]
+            collection = PatchCollection(patches, edgecolor='red', facecolor='none', linewidth=1)
+        ax.add_collection(collection)
+
+        # --- Save thumbnail ---
+        plt.savefig(thumbFn, dpi=80, bbox_inches=None, pad_inches=0, pil_kwargs={"compress_level": 4})
+        plt.close(fig)
+
+    def read_star_coordinates(self, posFn):
+        coords = []
+        with open(posFn) as f:
+            lines = f.readlines()
+
+        in_data_particles = False
+        for line in lines:
+            line = line.strip()
+            if not line or line.startswith('#'):
+                continue
+
+            if line.startswith('data_particles'):
+                in_data_particles = True
+                continue
+            if not in_data_particles:
+                continue
+
+            if line.startswith('loop_') or line.startswith('_'):
+                continue
+
+            parts = line.split()
+            if len(parts) >= 4:
+                x = float(parts[2])
+                y = float(parts[3])
+                coords.append((x, y))
+
+        return coords

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/protocols/protocol_extract_particles.py

@@ -182,12 +182,12 @@ class XmippProtExtractParticles(ProtExtractParticles, XmippProtocol):
                       help='Pixels outside this circle are assumed to be noise '
                            'and their stddev is set to 1. Radius for '
                            'background circle definition (in pix.). If this '
-                           'value is 0, then half the box size is used.')
+                           'value is less than or equal to 0, then half the box size is used.')
         
         form.addParam('patchSize', params.IntParam, default=-1, 
                       label='Patch size for the variance filter (px)', 
                       expertLevel=LEVEL_ADVANCED,
-                      help='Windows size to make the variance filtter and '
+                      help='Windows size to make the variance filter and '
                            'compute the Gini coeff. A twice of the particle '
                            'size is recommended. Set at -1 applies 1.5*BoxSize.')
 

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/protocols/protocol_extract_particles_pairs.py

@@ -158,7 +158,7 @@ class XmippProtExtractParticlesPairs(ProtExtractParticlesPair, XmippProtocol):
                            'phase flip is not recommended.')
         form.addParam('doNormalize', BooleanParam, default=True,
                       label='Normalize (Recommended)',
-                      help='It subtract a ramp in the gray values and '
+                      help='It subtracts a ramp in the gray values and '
                            'normalizes so that in the background there is 0 '
                            'mean and standard deviation 1.')
         form.addParam('normType', EnumParam,

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/protocols/protocol_preprocess/protocol_preprocess.py

@@ -157,8 +157,8 @@ class XmippProtPreprocessParticles(XmippProcessParticles):
                       help='Angstroms.')
         form.addParam('doNormalize', BooleanParam, default=False,
                       label='Normalize', 
-                      help='It subtract a ramp in the gray values and normalizes'
-                           'so that in the background there is 0 mean and'
+                      help='It subtracts a ramp in the gray values and normalizes '
+                           'so that in the background there is 0 mean and '
                            'standard deviation 1.')
         form.addParam('normType', EnumParam, condition='doNormalize',
                       label='Normalization type', expertLevel=LEVEL_ADVANCED,
@@ -169,10 +169,10 @@ class XmippProtPreprocessParticles(XmippProcessParticles):
                            'Ramp: subtract background + NewXmipp')
         form.addParam('backRadius', IntParam, default=-1, condition='doNormalize',
                       label='Background radius', expertLevel=LEVEL_ADVANCED,
-                      help='Pixels outside this circle are assumed to be noise and'
-                           'their stddev is set to 1. Radius for background'
-                           'circle definition (in pix.).'
-                           'If this value is 0, then half the box size is used.')
+                      help='Pixels outside this circle are assumed to be noise and '
+                           'their stddev is set to 1. Radius for background '
+                           'circle definition (in pix.). '
+                           'If this value is less than or equal to 0, then half the box size is used.')
         form.addParam('doCenter', BooleanParam, default=False,
                       label='Center images')
         form.addParam('doPhaseFlip', BooleanParam, default=False,

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/protocols.conf

@@ -63,8 +63,6 @@ Protocols SPA = [
 	{"tag": "section", "text": "2D", "children": [
 		{"tag": "protocol_group", "text": "Align", "openItem": "False", "children": [
 			{"tag": "protocol", "value": "XmippProtCL2DAlign",   "text": "default"},			
-			{"tag": "protocol", "value": "XmippProtDeepCenter",   "text": "default"},
-			{"tag": "protocol", "value": "XmippProtDeepCenterPredict",   "text": "default"},
 			{"tag": "protocol", "value": "XmippProtApplyAlignment",   "text": "default"},
 			{"tag": "section", "text": "more", "openItem": "False", "children": [
 				{"tag": "protocol", "value": "ProtAlignmentAssign", "text": "default"}

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/version.py

@@ -40,6 +40,6 @@ _binVersion = 'v4' # Increase it if major release is generated in xmipp
 # - If several of the above are true, only change the biggest one applicable (
 #   for example, if a fix is made and a new protocol are included in the same
 #   pull request, increase the one related to the new protocol).
-__version__ = '26.0.2'
+__version__ = '26.2.0'
 
-_currentDepVersion = '1.0'
+_currentDepVersion = '1.1'

{scipion_em_xmipp-26.0.2 → scipion_em_xmipp-26.2.0}/xmipp3/viewers/viewer_deep_micrograph_cleaner.py

@@ -34,7 +34,15 @@ from pyworkflow.viewer import DESKTOP_TKINTER, WEB_DJANGO, ProtocolViewer
 
 from pwem import emlib
 from xmipp3.convert import getXmippAttribute
-from xmipp3.protocols.protocol_deep_micrograph_screen import XmippProtDeepMicrographScreen
+from xmipp3.protocols.protocol_deep_micrograph_screen import XmippProtDeepMicrographScreen, NUM_THUMBNAILS
+from xmippLib import Image
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+from matplotlib.patches import Patch
+import matplotlib
+
 
 class XmippDeepMicrographViewer(ProtocolViewer):
     """         
@@ -61,10 +69,18 @@ class XmippDeepMicrographViewer(ProtocolViewer):
                            " to the threshold indicated in the box.\n"
                            "If you like the result, save the result"
                            " with the '+Coordinates' button")
-
+        form.addParam('visualizeMaskAndMic', LabelParam,
+                    label=f"Visualize {NUM_THUMBNAILS} micrographs with the mask and coords. overlayed",
+                    help="Visualize micrographs with the DeepMicrographCleaner mask "
+                         "overlayed using a color transparency and the coords stamp.\n"
+                         "The transparency and the color (blue to yellow) indicates the Deep score factor applied."
+                         f"Will be shown the first {NUM_THUMBNAILS} miccrographs."
+                         f"If aliasing arise is because the compresion of the thumbnails"
+        )
     def _getVisualizeDict(self):
         return {'visualizeCoordinates': self._visualizeCoordinates,
-                'visualizeHistogram': self._visualizeHistogram}
+                'visualizeHistogram': self._visualizeHistogram,
+                'visualizeMaskAndMic': self._visualizeMaskAndMic}
 
     def _visualizeCoordinates(self, e=None):
         views = []
@@ -119,8 +135,7 @@ class XmippDeepMicrographViewer(ProtocolViewer):
                 plotter.createSubPlot("Deep micrograph score",
                                       "Deep micrograph score",
                                       "Number of Coordinates")
-                cScores = [getXmippAttribute(coord, mdLabel).get()
-                           for coord in outCoords]
+                cScores = [getXmippAttribute(coord, mdLabel).get() for coord in outCoords]
                 plotter.plotHist(cScores, nbins=numberOfBins)
                 views.append(plotter)
             else:
@@ -129,3 +144,61 @@ class XmippDeepMicrographViewer(ProtocolViewer):
             print(" > Output not ready yet.")
 
         return views
+
+    def _visualizeMaskAndMic(self, e=None):
+        if not self.protocol.saveMicThumbnailWithMask.get():
+            return None
+
+        views = []
+        thumb_dir = self.protocol._getExtraPath('thumbnails')
+        thumbs = sorted([
+            os.path.join(thumb_dir, f)
+            for f in os.listdir(thumb_dir)
+            if f.lower().endswith('.png')
+        ])
+
+        if not thumbs:
+            return None
+
+        n = len(thumbs)
+        per_page = 15
+        cols = 5
+        rows = int(per_page / cols)
+
+        for page_start in range(0, n, per_page):
+            page_thumbs = thumbs[page_start:page_start + per_page]
+
+            fig = plt.figure(figsize=(cols * 5, rows * 5))
+            gs = matplotlib.gridspec.GridSpec(rows, cols, figure=fig, wspace=0.05, hspace=0.08)
+
+            axes = []
+            for i in range(rows * cols):
+                r, c = divmod(i, cols)
+                ax = fig.add_subplot(gs[r, c])
+                ax.axis('off')
+                axes.append(ax)
+
+            for i, fn in enumerate(page_thumbs):
+                img = mpimg.imread(fn)
+                axes[i].imshow(img)
+
+            for i in range(len(page_thumbs), rows * cols):
+                fig.delaxes(axes[i])
+
+            cmap = plt.get_cmap('YlGnBu')
+            norm = matplotlib.colors.Normalize(vmin=0, vmax=1)
+            sm = matplotlib.cm.ScalarMappable(cmap=cmap, norm=norm)
+            sm.set_array([])
+
+            cbar_ax = fig.add_axes([0.2, 0.05, 0.5, 0.02])
+            cbar = fig.colorbar(sm, cax=cbar_ax, orientation='horizontal')
+            cbar.set_label('Mask deep score')
+
+            try:
+                fig.canvas.manager.set_window_title(f'Thumbnails {page_start + 1}-{page_start + len(page_thumbs)}'  )
+            except AttributeError:
+                pass
+
+            views.append(fig)
+
+        return views