First commit of Flexutils-Scripts

Author: DavidHerreros

.gitignore

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+# Python compilation files
+*.pyc
+
+# Ignore temporary packaging folder
+*.egg-info
+toolkit/*.egg-info
+
+# IDE files
+.idea

CHANGES.txt

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+include LICENSE
+include requirement/*.yml
+include icon_square.png
+include scripts/*.py
+include socket/*.py
+include viewers/*.py
+include *.sh
+include *.rst
+include *.txt
+include *.py

LICENSE

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+=======================
+Flexutils Scripts
+=======================
+
+This package provides a the environment and scripts needed by `scipion-em-flexutils <https://github.com/scipion-em/scipion-em-flexutils>`_ plugin

MANIFEST.in

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+# **************************************************************************
+# *
+# * Authors:     David Herreros Calero ([email protected])
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+
+
+import os
+import sys
+import subprocess
+
+
+__version__ = "1.0.0"
+
+
+def getImagePath(image_name):
+    """Returns the absolute path to an image within the package."""
+    module_dir = os.path.dirname(__file__)  # Get the directory of this module
+    image_path = os.path.join(module_dir, 'media', image_name)
+    return image_path
+
+def getCondaBase():
+    try:
+        conda_base = subprocess.check_output("conda info --base", shell=True, text=True).strip()
+        return conda_base
+    except subprocess.CalledProcessError as e:
+        print(f"Error finding Conda base: {e}")
+        return None
+
+def getCondaSourceFile():
+    conda_source_file = f"{getCondaBase()}/etc/profile.d/conda.sh"
+    return conda_source_file
+
+def getProgram(program, env_name=None):
+    env_name = env_name if env_name is not None else f"flexutils-{__version__}"
+    return f"source {getCondaSourceFile()} && conda activate {env_name} && python {program}"
+
+def runProgram(program, args, env=None, cwd=None):
+    command = program + " " + args
+    subprocess.check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
+                          env=env, cwd=cwd)

README.rst

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+# **************************************************************************
+# *
+# * Authors:     David Herreros Calero ([email protected])
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+

flexutils_scripts/__init__.py

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+# **************************************************************************
+# *
+# * Authors:  David Herreros Calero ([email protected])
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+
+
+from flexutils_scripts import utils as utl
+
+
+def alignMaps(file_input, file_target, file_output, global_search=None):
+    # Align maps in ChimeraX using fitmap
+    _ = utl.alignMapsChimeraX(file_input, file_target, global_search=global_search,
+                              output_map=file_output)
+
+
+if __name__ == '__main__':
+    import argparse
+
+    # Input parameters
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--i', type=str, required=True)
+    parser.add_argument('--r', type=str, required=True)
+    parser.add_argument('--o', type=str, required=True)
+    parser.add_argument('--gs', type=int)
+
+    args = parser.parse_args()
+
+    if args.gs is None:
+        gs = None
+    else:
+        gs = args.gs
+
+    # Initialize volume slicer
+    alignMaps(args.i, args.r, args.o, gs)

flexutils_scripts/media/chimerax_logo.png

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+# **************************************************************************
+# *
+# * Authors:     David Herreros Calero ([email protected])
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+
+
+import numpy as np
+from pathlib import Path
+import prody as pd
+from scipy.ndimage import gaussian_filter
+from xmipp_metadata.image_handler import ImageHandler
+
+from flexutils_scripts import utils as utl
+
+
+def apply_deformation_field_zernike3d(ref_file, vol_file, z_file, out_file, boxsize, sr):
+    ref_file = Path(ref_file)
+
+    # Get coords
+    if ref_file.suffix in [".mrc", ".vol"]:
+        mode = "volume"
+        mask = ImageHandler(ref_file).getData()
+        volume = ImageHandler(vol_file).getData()
+        indices = np.asarray(np.where(mask > 0))
+        indices = np.transpose(np.asarray([indices[2, :], indices[1, :], indices[0, :]]))
+        coords = indices - 0.5 * boxsize
+        groups = mask[indices[:, 2], indices[:, 1], indices[:, 0]]
+        values = volume[indices[:, 2], indices[:, 1], indices[:, 0]]
+
+        if np.unique(groups).size > 1:
+            centers = []
+            for group in np.unique(groups):
+                centers.append(np.mean(coords[groups == group], axis=0))
+            centers = np.asarray(centers)
+        else:
+            groups, centers = None, None
+
+    elif ref_file.suffix in [".pdb", ".cif"]:
+        mode = "structure"
+        pd_struct = pd.parsePDB(str(ref_file), subset=None, compressed=False)
+        coords = pd_struct.getCoords()
+        centers = None
+        groups = None
+
+    # Read Zernike params
+    basis_params, A = utl.readZernikeFile(z_file)
+    L1, L2, r = basis_params
+    r = sr * r if mode == "structure" else r
+
+    # Zernike coefficients
+    A = utl.resizeZernikeCoefficients(A.reshape(-1))
+    A = sr * A if mode == "structure" else A
+
+    # Compute basis
+    Z = utl.computeBasis(L1=int(L1), L2=int(L2), pos=coords, r=r, groups=groups, centers=centers)
+
+    # Compute deformation field
+    d_f = Z @ A.T
+
+    # Apply deformation field
+    if mode == "volume":
+        indices_moved = np.round(indices + d_f).astype(int)
+
+        # Scatter in volume
+        def_vol = np.zeros((boxsize, boxsize, boxsize))
+        for idx in range(indices_moved.shape[0]):
+            if np.all(np.abs(indices_moved[idx]) < boxsize):
+                def_vol[indices_moved[idx, 2], indices_moved[idx, 1], indices_moved[idx, 0]] += values[idx]
+        # np.add.at(def_vol, [indices_moved[:, 2], indices_moved[:, 1], indices_moved[:, 0]], 1)
+
+        # Gaussian filter map
+        def_vol = gaussian_filter(def_vol, sigma=1.0)
+
+        # Save results
+        ImageHandler().write(def_vol, filename=out_file, overwrite=True, sr=sr)
+
+    elif mode == "structure":
+        # Move coords
+        coords_moved = coords + d_f
+
+        # Save results
+        pd_struct_out = pd_struct.copy()
+        pd_struct_out.setCoords(coords_moved)
+        pd.writePDB(out_file, pd_struct_out, hybrid36=True)
+
+
+if __name__ == '__main__':
+    import argparse
+
+    # Input parameters
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--ref_file', type=str, required=True)
+    parser.add_argument('--vol_file', type=str, required=True)
+    parser.add_argument('--z_file', type=str, required=True)
+    parser.add_argument('--out_file', type=str, required=True)
+    parser.add_argument('--boxsize', type=int, required=True)
+    parser.add_argument('--sr', type=float, required=True)
+
+    args = parser.parse_args()
+
+    # Initialize volume slicer
+    apply_deformation_field_zernike3d(args.ref_file, args.vol_file, args.z_file, args.out_file,
+                                      args.boxsize, args.sr)

flexutils_scripts/media/icon_square.png

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+# **************************************************************************
+# *
+# * Authors:  David Herreros Calero ([email protected])
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * 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 '[email protected]'
+# *
+# **************************************************************************
+
+
+import numpy as np
+import pickle
+from shapely.geometry import Point
+
+
+def checkInROI(coords, polygons_file, outFile):
+    # Define polygons based on selected borders
+    with open(polygons_file, "rb") as f:
+        polygons = pickle.load(f)
+
+    in_area_vec = []
+    for coord in coords:
+        in_area = 0
+        point = Point(coord[0], coord[1])
+        for polygon in polygons:
+            if polygon.contains(point):
+                in_area = 1
+                break
+        in_area_vec.append(in_area)
+
+    np.savetxt(outFile, np.asarray(in_area_vec))
+
+
+if __name__ == '__main__':
+    import argparse
+
+    # Input parameters
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input', type=str, required=True)
+    parser.add_argument('--polygons', type=str, required=True)
+    parser.add_argument('--output', type=str, required=True)
+
+    args = parser.parse_args()
+
+    coords = np.loadtxt(args.input, delimiter=' ')
+
+    # Initialize volume slicer
+    checkInROI(coords, args.polygons, args.output)