pyTEMlib 0.2020.11.1__py3-none-any.whl → 0.2024.8.4__py3-none-any.whl

pyTEMlib/atom_tools.py

@@ -1,245 +1,240 @@
-"""
-All atom detection is done here
-
-Everything is in unit of pixel!!
-"""
-# All atom detection is done here
-# Everything is in unit of pixel!!
-#
-
-import numpy as np
-
-from skimage.feature import peak_local_max
-from sklearn.cluster import KMeans
-from scipy.spatial import cKDTree
-import scipy.optimize as optimization
-
-from .probe_tools import *
-from .file_tools import *
-
-
-def find_atoms(image, tags):
-    """
-    Find atoms
-
-    Not changed to sidpy dataset yet.
-    """
-    image = image - image.min()
-    image = image / image.max()
-
-    if 'sigma_min' not in tags:
-        tags['sigma_min'] = 0.1
-    if 'resolution' not in tags:
-        tags['resolution'] = 0.1
-
-    if 'ROIsize' not in tags:
-        tags['ROIsize'] = 100.
-
-    res = tags['resolution'] / tags['pixel_size']  # * tags['ROIsize']/100.
-    print('res', res)
-    coordinates = peak_local_max(image, min_distance=int(res / 2), threshold_rel=tags['sigma_min'], exclude_border=True)
-    print('coor', len(coordinates))
-    """
-       peak_local_max(image, min_distance=10, threshold_abs=0, threshold_rel=0.1,
-                   exclude_border=True, indices=True, num_peaks=np.inf,
-                   footprint=None, labels=None):
-
-        Find peaks in an image, and return them as coordinates or a boolean array.
-        Peaks are the local maxima in a region of `2 * min_distance + 1
-
-        (i.e. peaks are separated by at least `min_distance`).
-        NOTE: If peaks are flat (i.e. multiple adjacent pixels have identical
-        intensities), the coordinates of all such pixels are returned.
-    """
-
-    # We calculate the radius in pixel of a round area in which atoms are evaluated
-    sc = tags['pixel_size']
-    r = tags['resolution'] / sc * tags['ROIsize'] / 100. / 2.
-    tags['radius'] = r
-
-    #######################################
-    # Now we determine intensity #
-    #######################################
-
-    ###############
-    # Make a circular mask for integration of atom intensity
-    ################
-    rr = int(r + 0.5)
-    mask = np.zeros((2 * rr + 1, 2 * rr + 1))
-
-    for i in range(2 * rr + 1):
-        for j in range(2 * rr + 1):
-            if (i - rr) ** 2 + (j - rr) ** 2 < rr ** 2 + 0.1:
-                mask[i, j] = 1
-
-    ###
-    # Determine  pixel position and intensity  of all atoms
-    ###
-    atoms = []
-    for i in range(len(coordinates)):
-        x, y = coordinates[i]
-
-        if rr < x < image.shape[1] - rr and rr < y < image.shape[0] - rr:
-            area = image[x - rr:x + rr + 1, y - rr:y + rr + 1]
-            arr = area * mask
-            atoms.append((x, y, rr, arr.sum(), arr.max()))
-
-    print(' Detected ', len(atoms), ' atoms')
-    atoms.sort()
-    return atoms
-
-
-def atoms_clustering(atoms, mid_atoms, number_of_clusters=3, nearest_neighbours=7):
-    """
-    KMeans clustering of atoms according to nearest neighbour distances
-
-    Input:
-        atoms: (nx2) numpy array or list of floats with atom positions
-        mid-atoms: list of indices of atoms not at rim
-    Optional:
-        number_of_clusters: number of output clusters (default=3)
-        nearest_neighbours: number of nearest neighbours to be considered (default=7)
-    """
-    # get distances
-    nn_tree = cKDTree(np.array(atoms)[:, 0:2])
-
-    distances, indices = nn_tree.query(np.array(mid_atoms)[:, 0:2], nearest_neighbours)
-
-    # Clustering
-    k_means = KMeans(n_clusters=number_of_clusters, random_state=0)  # Fixing the RNG in kmeans
-    k_means.fit(distances)
-    clusters = k_means.predict(distances)
-    return clusters, distances, indices
-
-
-def gauss_difference(params, area):
-    """
-    difference between Gaussian and area in image
-
-    used in atom_refine function
-    """
-    gauss = make_gauss(area.shape[0], area.shape[1], width=params[0], x0=params[1], y0=params[2], intensity=params[3])
-    return (area - gauss).flatten()
-
-
-def atom_refine(image, atoms, radius, max_int=0, min_int=0, max_dist=4):
-    """
-        fits a Gaussian in a blob
-    """
-    rr = int(radius + 0.5)  # atom radius
-    print('using radius ', rr, 'pixels')
-
-    pixels = np.linspace(0, 2 * rr, 2 * rr + 1) - rr
-    x, y = np.meshgrid(pixels, pixels)
-    mask = (x ** 2 + y ** 2) < rr ** 2
-
-    guess = [rr * 2, 0.0, 0.0, 1]
-
-    sym = {'number_of_atoms': len(atoms)}
-
-    volume = []
-    position = []
-    intensities = []
-    maximum_area = []
-    new_atoms = []
-    gauss_width = []
-    gauss_amplitude = []
-    gauss_intensity = []
-    if QT_available:
-        progress = pyTEMlib.sidpy_tools.ProgressDialog("Refine Atom Positions", len(atoms))
-
-    done = 0
-    for i in range(len(atoms)):
-        if QT_available:
-            progress.set_value(i)
-
-        else:
-            if done < int((i + 1) / len(atoms) * 50):
-                done = int((i + 1) / len(atoms) * 50)
-                sys.stdout.write('\r')
-                # progress output :
-                sys.stdout.write("[%-50s] %d%%" % ('=' * done, 2 * done))
-                sys.stdout.flush()
-
-        x, y = atoms[i][0:2]
-        x = int(x)
-        y = int(y)
-
-        area = image[x - rr:x + rr + 1, y - rr:y + rr + 1]
-
-        append = False
-
-        if (x - rr) < 0 or y - rr < 0 or x + rr + 1 > image.shape[0] or y + rr + 1 > image.shape[1]:
-            position.append(-1)
-            intensities.append(0)
-            maximum_area.append(0)
-        else:
-            position.append(1)
-            intensities.append((area * mask).sum())
-            maximum_area.append((area * mask).max())
-
-        if max_int > 0:
-            if area.sum() < max_int:
-                if area.sum() > min_int:
-                    append = True
-        elif area.sum() > min_int:
-            append = True
-
-        pout = [0, 0, 0, 0]
-        if append:
-            if (x - rr) < 0 or y - rr < 0 or x + rr + 1 > image.shape[0] or y + rr + 1 > image.shape[1]:
-                pass
-            else:
-                [pout, _] = optimization.leastsq(gauss_difference, np.array(guess), args=area)
-
-            if (abs(pout[1]) > max_dist) or (abs(pout[2]) > max_dist):
-                pout = [0, 0, 0, 0]
-
-        volume.append(2 * np.pi * pout[3] * pout[0] * pout[0])
-
-        new_atoms.append([x + pout[1], y + pout[2]])  # ,pout[0],  volume)) #,pout[3]))
-        if all(v == 0 for v in pout):
-            gauss_intensity.append(0.)
-        else:
-            gauss = make_gauss(area.shape[0], area.shape[1], width=pout[0], x0=pout[1], y0=pout[2], intensity=pout[3])
-            gauss_intensity.append((gauss * mask).sum())
-        gauss_width.append(pout[0])
-        gauss_amplitude.append(pout[3])
-    if QT_available:
-        progress.close()
-
-    sym['inside'] = position
-    sym['intensity_area'] = intensities
-    sym['maximum_area'] = maximum_area
-    sym['atoms'] = new_atoms
-    sym['gauss_width'] = gauss_width
-    sym['gauss_amplitude'] = gauss_amplitude
-    sym['gauss_intensity'] = gauss_intensity
-    sym['gauss_volume'] = volume
-
-    return sym
-
-
-def intensity_area(image, atoms, radius=3):
-    """
-    Intensity of atoms
-
-    Intensity of atoms in an image within a disk of radius
-    """
-
-    rr = int(radius + 0.5)  # atom radius
-    print('using radius ', rr, 'pixels')
-
-    pixels = np.linspace(0, 2 * rr, 2 * rr + 1) - rr
-    x, y = np.meshgrid(pixels, pixels)
-    mask = (x ** 2 + y ** 2) < rr ** 2
-    intensities = []
-    for i in range(len(atoms)):
-        x = int(atoms[i][1])
-        y = int(atoms[i][0])
-        area = image[x - rr:x + rr + 1, y - rr:y + rr + 1]
-        if area.shape == mask.shape:
-            intensities.append((area * mask).sum())
-        else:
-            intensities.append(-1)
-    return intensities
+""" Atom detection
+
+All atom detection is done here
+Everything is in unit of pixel!!
+
+Author: Gerd Duscher
+
+part of pyTEMlib
+
+a pycroscopy package
+"""
+
+import numpy as np
+import sys
+
+# from skimage.feature import peak_local_max
+from skimage.feature import blob_log
+
+from sklearn.cluster import KMeans
+from scipy.spatial import cKDTree
+import scipy.optimize as optimization
+
+import pyTEMlib.probe_tools as probe_tools
+import pyTEMlib.file_tools as ft
+import sidpy
+from tqdm.auto import trange
+
+
+def find_atoms(image, atom_size=0.1, threshold=0.):
+    """ Find atoms is a simple wrapper for blob_log in skimage.feature
+
+    Parameters
+    ----------
+    image: sidpy.Dataset
+        the image to find atoms
+    atom_size: float
+        visible size of atom blob diameter in nm gives minimal distance between found blobs
+    threshold: float
+        threshold for blob finder; (usually between 0.001 and 1.0) for threshold <= 0 we use the RMS contrast
+
+    Returns
+    -------
+    atoms: numpy array(Nx3)
+        atoms positions and radius of blob
+    """
+
+    if not isinstance(image, sidpy.Dataset):
+        raise TypeError('We need a sidpy.Dataset')
+    if image.data_type.name != 'IMAGE':
+        raise TypeError('We need sidpy.Dataset of sidpy.Datatype: IMAGE')
+    if not isinstance(atom_size, (float, int)):
+        raise TypeError('atom_size parameter has to be a number')
+    if not isinstance(threshold, float):
+        raise TypeError('threshold parameter has to be a float number')
+
+    scale_x = ft.get_slope(image.dim_0)
+    im = np.array(image-image.min())
+    im = im/im.max()
+    if threshold <= 0.:
+        threshold = np.std(im)
+    atoms = blob_log(im, max_sigma=atom_size/scale_x, threshold=threshold)
+
+    return atoms
+
+
+def atoms_clustering(atoms, mid_atoms, number_of_clusters=3, nearest_neighbours=7):
+    """ A wrapper for sklearn.cluster kmeans clustering of atoms.
+
+    Parameters
+    ----------
+    atoms: list or np.array (Nx2)
+        list of all atoms
+    mid_atoms: list or np.array (Nx2)
+        atoms to be evaluated
+    number_of_clusters: int
+        number of clusters to sort (ini=3)
+    nearest_neighbours: int
+        number of nearest neighbours evaluated
+
+    Returns
+    -------
+    clusters, distances, indices: numpy arrays
+    """
+
+    # get distances
+    nn_tree = cKDTree(np.array(atoms)[:, 0:2])
+
+    distances, indices = nn_tree.query(np.array(mid_atoms)[:, 0:2], nearest_neighbours)
+
+    # Clustering
+    k_means = KMeans(n_clusters=number_of_clusters, random_state=0)  # Fixing the RNG in kmeans
+    k_means.fit(distances)
+    clusters = k_means.predict(distances)
+
+    return clusters, distances, indices
+
+
+def gauss_difference(params, area):
+    """
+    Difference between part of an image and a Gaussian
+    This function is used int he atom refine function of pyTEMlib
+
+    Parameters
+    ----------
+    params: list
+        list of Gaussian parameters [width, position_x, position_y, intensity]
+    area:  numpy array
+        2D matrix = part of an image
+
+    Returns
+    -------
+    numpy array: flattened array of difference
+
+    """
+    gauss = probe_tools.make_gauss(area.shape[0], area.shape[1], width=params[0], x0=params[1], y0=params[2],
+                                   intensity=params[3])
+    return (area - gauss).flatten()
+
+
+def atom_refine(image, atoms, radius, max_int=0, min_int=0, max_dist=4):
+    """Fits a Gaussian in a blob of an image
+
+    Parameters
+    ----------
+    image: np.array or sidpy Dataset
+    atoms: list or np.array
+        positions of atoms
+    radius: float
+        radius of circular mask to define fitting of Gaussian
+    max_int: float
+        optional - maximum intensity to be considered for fitting (to exclude contaminated areas for example)
+    min_int: float
+        optional - minimum intensity to be considered for fitting (to exclude contaminated holes for example)
+    max_dist: float
+        optional - maximum distance of movement of Gaussian during fitting
+
+    Returns
+    -------
+    sym: dict
+        dictionary containing new atom positions and other output such as intensity of the fitted Gaussian
+    """
+    rr = int(radius + 0.5)  # atom radius
+    print('using radius ', rr, 'pixels')
+
+    pixels = np.linspace(0, 2 * rr, 2 * rr + 1) - rr
+    x, y = np.meshgrid(pixels, pixels)
+    mask = (x ** 2 + y ** 2) < rr ** 2
+
+    guess = [rr * 2, 0.0, 0.0, 1]
+
+    sym = {'number_of_atoms': len(atoms)}
+
+    volume = []
+    position = []
+    intensities = []
+    maximum_area = []
+    new_atoms = []
+    gauss_width = []
+    gauss_amplitude = []
+    gauss_intensity = []
+
+    for i in trange(len(atoms)):
+        x, y = atoms[i][0:2]
+        x = int(x)
+        y = int(y)
+
+        area = image[x - rr:x + rr + 1, y - rr:y + rr + 1]
+
+        append = False
+
+        if (x - rr) < 0 or y - rr < 0 or x + rr + 1 > image.shape[0] or y + rr + 1 > image.shape[1]:  # atom not found
+            position.append(-1)
+            intensities.append(-1.)
+            maximum_area.append(-1.)
+        else:  # atom found
+            position.append(1)
+            intensities.append((area * mask).sum())
+            maximum_area.append((area * mask).max())
+
+        if max_int > 0:
+            if area.sum() < max_int:
+                if area.sum() > min_int:
+                    append = True
+        elif area.sum() > min_int:
+            append = True
+
+        pout = [0, 0, 0, 0]
+        if append:
+            if (x - rr) < 0 or y - rr < 0 or x + rr + 1 > image.shape[0] or y + rr + 1 > image.shape[1]:
+                pass
+            else:
+                [pout, _] = optimization.leastsq(gauss_difference, guess, args=area)
+
+            if (abs(pout[1]) > max_dist) or (abs(pout[2]) > max_dist):
+                pout = [0, 0, 0, 0]
+
+        volume.append(2 * np.pi * pout[3] * pout[0] * pout[0])
+
+        new_atoms.append([x + pout[1], y + pout[2]])  # ,pout[0],  volume)) #,pout[3]))
+        if all(v == 0 for v in pout):
+            gauss_intensity.append(0.)
+        else:
+            gauss = probe_tools.make_gauss(area.shape[0], area.shape[1], width=pout[0], x0=pout[1], y0=pout[2],
+                                           intensity=pout[3])
+            gauss_intensity.append((gauss * mask).sum())
+        gauss_width.append(pout[0])
+        gauss_amplitude.append(pout[3])
+
+    sym['inside'] = position
+    sym['intensity_area'] = intensities
+    sym['maximum_area'] = maximum_area
+    sym['atoms'] = new_atoms
+    sym['gauss_width'] = gauss_width
+    sym['gauss_amplitude'] = gauss_amplitude
+    sym['gauss_intensity'] = gauss_intensity
+    sym['gauss_volume'] = volume
+
+    return sym
+
+
+def intensity_area(image, atoms, radius):
+    """
+    integrated intensity of atoms in an image with a mask around each atom of radius radius
+    """
+    rr = int(radius + 0.5)  # atom radius
+    print('using radius ', rr, 'pixels')
+
+    pixels = np.linspace(0, 2 * rr, 2 * rr + 1) - rr
+    x, y = np.meshgrid(pixels, pixels)
+    mask = np.array((x ** 2 + y ** 2) < rr ** 2)
+    intensities = []
+    for i in range(len(atoms)):
+        x = int(atoms[i][1])
+        y = int(atoms[i][0])
+        area = image[x - rr:x + rr + 1, y - rr:y + rr + 1]
+        if area.shape == mask.shape:
+            intensities.append((area * mask).sum())
+        else:
+            intensities.append(-1)
+    return intensities

pyTEMlib/config_dir.py

@@ -1,33 +1,57 @@
-# -*- coding: utf-8 -*-
-"""
-Provides access to the configuration directory of pyTEMlib
-"""
-
-# Gleaned from
-# Copyright © 2007 Francisco Javier de la Peña
-# file of EELSLab.
-#
-
-import os
-import shutil
-
-config_files = ['TEMlibrc', 'microscopes.csv', 'edges_db.csv', 'edges_db.pkl', 'fparam.txt']
-data_path = os.sep.join([os.path.dirname(__file__), 'data'])
-
-if os.name == 'posix':
-    config_path = os.path.join(os.path.expanduser('~'), '.TEMlib')
-    os_name = 'posix'
-elif os.name in ['nt', 'dos']:
-    config_path = os.path.join(os.path.expanduser('~'), '.TEMlib')
-    os_name = 'windows'
-else:
-    config_path = '.'
-if os.path.isdir(config_path) is False:
-    # messages.information("Creating config directory: %s" % config_path)
-    os.mkdir(config_path)
-    
-for file in config_files:
-    templates_file = os.path.join(data_path, file)
-    config_file = os.path.join(config_path, file)
-    if os.path.isfile(config_file) is False:
-        shutil.copy(templates_file, config_file)
+# -*- coding: utf-8 -*-
+# part of pyTEMlib
+# 2022/08 Changed this to be hopefully compatible with conda-forge
+#
+#
+"""
+config_dir: setup of directory ~/.pyTEMlib for custom sources and database
+"""
+import os
+
+# import wget
+if os.name == 'posix':
+    config_path = os.path.join(os.path.expanduser('~'), '.pyTEMlib')
+    os_name = 'posix'
+elif os.name in ['nt', 'dos']:
+    config_path = os.path.join(os.path.expanduser('~'), '.pyTEMlib')
+    os_name = 'windows'
+else:
+    config_path = '.'
+
+if os.path.isdir(config_path) is False:
+    # messages.information("Creating config directory: %s" % config_path)
+    os.mkdir(config_path)
+
+lines = ['Microscope,E0,alpha,beta,pppc,correlation_factor,VOA_conv,EELS_b1,EELS_b2,EELS_b100,MADF_offset,MADF_slope,'
+         'HADF_offset,HADF_slope,BF_offset,BF_slope',
+         'Libra 200,2.00E+05,10,15,1,1,6241509.647,0.0634,0.0634,0.0634,0,0,0,0,0,0',
+         'UltraSTEM 60,6.00E+04,30,50,1,1,1.79E+07,0.2,0.45,0.9,0.001383,4.04E-06,0,0,0,0',
+         'UltraSTEM 100,1.00E+05,30,50,1,1,6.24E+06,0.45,1,2,0,0,0,0,0,0',
+         'UltraSTEM 200,2.00E+05,30,50,1,1,6.24E+06,0.45,1,2,0,0,0,0,0,0']
+
+config_file = os.path.join(config_path, 'microscopes.csv')
+if os.path.isfile(config_file) is False:  # Do not overwrite users microscopy files
+    with open(config_file, 'w') as f:
+        f.write('\n'.join(lines))
+
+""" 
+import pickle
+from pkg_resources import resource_filename
+
+data_path = resource_filename(__name__, 'data')
+pkl_file = open(data_path + '/old/edges_db.pkl', 'rb')
+x_sections = pickle.load(pkl_file)
+pkl_file.close()
+for key in range(80, 83):
+    print(f'\'{key}\': ', x_sections[str(key)], ',')
+
+# config_file = os.path.join(config_path, 'edges_db.pkl')
+ref = importlib_resources.files('pyTEMlib') / 'data/edges_db.pkl'
+with importlib_resources.as_file(ref) as templates_file:
+    if os.path.isfile(config_file) is False:
+        try:
+            shutil.copy(templates_file, config_file)
+        except FileNotFoundError:
+            pass
+            # wget('https://github.com/pycroscopy/pyTEMlib/tree/main/pyTEMlib/data/'+file)
+"""