alignfaces 1.0.1__py3-none-any.whl

alignfaces/make_aligned_faces.py

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+from .face_landmarks import (facial_landmarks, pull_jawline_to_inside_of_hairline,
+                            unpack_dict_to_vector_xy, pack_vector_xy_as_dict)
+
+from math import floor, ceil
+
+# import matplotlib.pyplot as plt
+import numpy as np
+import math
+import os.path
+from pathlib import Path
+
+# image io and grayscale conversion
+from PIL import Image as PilImage
+
+# image translation and rotation
+from skimage.transform import SimilarityTransform, warp
+
+# image scaling
+import dlib
+
+# Procrustes analysis
+# import procrustesTool as pt
+# from .procrustes_tools import procrustes_tools as pt
+from .procrustes_tools import (get_translation,
+                              generalized_procrustes_analysis,
+                              translate, get_rotation_scale,
+                              procrustes_analysis)
+
+# from .apertureTools import (fit_ellipse_semi_minor, make_ellipse_map,
+#                             make_circle_map, make_map_below_y,
+#                             make_moss_egg, make_four_channel_image)
+
+from .aperture_tools import (fit_ellipse_semi_minor, make_ellipse_map,
+                            make_moss_egg, make_four_channel_image)
+
+from .warp_tools import pawarp
+
+from .contrast_tools import contrast_stretch
+
+from .plot_tools import (plot_faces_with_landmarks,
+                         plot_faces_with_landmarks_one_by_one,
+                         fit_ellipse_to_2D_cloud,
+                         plot_ellipse)
+
+# import pdb  # TEMPORARY FOR DEBUGGING
+# Final adjustments and saving image
+from skimage import exposure
+from skimage.io import imsave
+
+# files
+import pickle
+import os
+import json
+import io
+import csv
+
+# testing
+import sys
+
+# additional functions
+from .make_files import get_source_files, clone_directory_tree
+
+# adjust_size = 'default'
+# size_value = None
+# start_fresh = True
+# iris_by_coherence = False
+
+# -----------------------------------------------------------------------------
+# Support function
+def get_rotation_matrix_2d(center, angle):
+    (x0, y0) = center[0], center[1]
+    M = np.array([[np.cos(angle), -np.sin(angle),
+                   x0*(1 - np.cos(angle)) + y0*np.sin(angle)],
+                  [np.sin(angle),  np.cos(angle),
+                   y0*(1 - np.cos(angle)) - x0*np.sin(angle)],
+                  [0, 0, 1]])
+    return M
+
+# -----------------------------------------------------------------------------
+# adjust_size, size_value -> only in 1st section, which is not necessary here.
+# color_of_result -> 303
+#
+# actually required:
+#   MotherDir, start_fresh, iris_by_coherence
+
+
+def get_landmarks(MotherDir, file_prefix, file_postfix, include_jaw=False,
+                  start_fresh=True):
+
+    # files = make_files(MotherDir, file_prefix, file_postfix)
+    # source_files = files[0]
+    # output_files = files[1]
+    source_files = get_source_files(MotherDir, FilePrefix=file_prefix,
+                                    FilePostfix=file_postfix)
+
+    # adjust_size='default', size_value=None, color_of_result='grayscale'
+
+    # MotherDir = "/Users/carl/Studies/Collaborations/Eugenie/RawFacesCleaned/"
+    # MotherDir = "/Users/carl/Studies/your_project_here/faces/"
+    # viewpoint = 'all'  # 'front', 'left', 'right'
+
+    # Copy directory structure for output
+    MotherBits = MotherDir.split(os.path.sep)
+    go_back = -len(MotherBits[-2]) - 1
+    GrannyDir = MotherDir[0:go_back]
+    file_results_temporary = MotherDir + "results_temporary.dat"
+    file_results = MotherDir + "results.dat"
+
+    if start_fresh:
+        try:
+            with open(file_results_temporary, "rb") as f:
+                print(file_results_temporary + "\t exists.\nRemoving ...")
+            os.remove(file_results_temporary)
+        except IOError as error:
+            print(error)
+
+    # To do: User interface for getting this, or simple arguments into script
+    keys_to_remove_for_alignment = ['JAWLINE_POINTS']
+
+    # try:
+    #     f = open(file_results_aligned, "rb")
+    #     data2 = []
+    #     for _ in range(pickle.load(f)):
+    #         data2.append(pickle.load(f))
+    #     LabelToCoordinateIndex = data2[0]
+    #     output_files = data2[1]
+    #     FinalLandmarks = data2[2]
+    #     f.close()
+    # except:
+    ###########################################################################
+    # input and output files
+    # with open(GrannyDir + 'input_files.data', 'rb') as filehandle:
+    #     source_files = pickle.load(filehandle)
+    # with open(GrannyDir + 'output_files.data', 'rb') as filehandle:
+    #     output_files = pickle.load(filehandle)
+
+    ###########################################################################
+    # Main
+
+    # Obtain facial landmarks and center-point for all faces
+    try:
+        with open(file_results_temporary, "rb") as f:
+            data_in = []
+            for _ in range(pickle.load(f)):
+                data_in.append(pickle.load(f))
+            AllSubjectsLandmarksDict = data_in[0]
+            AllSubjectsLandmarksDictAllFeature = data_in[1]
+            MeanXY = data_in[2]
+            LandmarkFailureFile = data_in[3]
+            LandmarkFailureIndex = data_in[4]
+            StartingIndex = len(MeanXY) + len(LandmarkFailureFile)
+            IrisPoints = data_in[5]
+    except IOError as error:
+        print(error)
+        AllSubjectsLandmarksDict = []
+        AllSubjectsLandmarksDictAllFeature = []
+        MeanXY = []
+        LandmarkFailureFile = []
+        LandmarkFailureIndex = []
+        StartingIndex = 0
+        IrisPoints = []
+
+    # for infile, outfile, facei in zip(source_files[StartingIndex:], output_files[StartingIndex:], range(StartingIndex, len(source_files))):
+    for infile, facei in zip(source_files[StartingIndex:], range(StartingIndex, len(source_files))):
+        # image = cv2.imread(infile)
+        # gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
+        gray = np.array(PilImage.open(infile).convert("L"))
+        Landmarks = facial_landmarks(gray)
+
+        if Landmarks is None:
+            print("Landmarks is None: " + str(facei))
+            LandmarkFailureFile.append(infile)
+            LandmarkFailureIndex.append(facei)
+            # AllSubjectsLandmarksDictAllFeature.append(np.array(CoordinateVector))
+            #
+            # AllSubjectsLandmarksDict.append(np.array(CoordinateVector))
+            #
+            # MeanXY.append(np.array([None, None]))
+        else:
+            le = Landmarks['LEFT_EYE_POINTS']
+            re = Landmarks['RIGHT_EYE_POINTS']
+            mle = le.mean(axis=0)
+            mre = re.mean(axis=0)
+            temp_dict = {0: (int(mre[1]), int(mre[0])),
+                         1: (int(mle[1]), int(mle[0]))}
+            IrisPoints.append(temp_dict)
+
+            Landmarks = pull_jawline_to_inside_of_hairline(Landmarks, gray)
+            CoordinateVector, LabelToCoordinateIndexAll = unpack_dict_to_vector_xy(Landmarks)
+            AllSubjectsLandmarksDictAllFeature.append(np.array(CoordinateVector))
+
+            for this_key in keys_to_remove_for_alignment:
+                Landmarks.pop(this_key, None)
+
+            CoordinateVector, LabelToCoordinateIndex = unpack_dict_to_vector_xy(Landmarks)
+            AllSubjectsLandmarksDict.append(np.array(CoordinateVector))
+
+            mean_x, mean_y = get_translation(CoordinateVector)
+            MeanXY.append(np.array([mean_x, mean_y]))
+
+        f = open(file_results_temporary, "wb")
+        data = [AllSubjectsLandmarksDict, AllSubjectsLandmarksDictAllFeature, MeanXY, LandmarkFailureFile, LandmarkFailureIndex, IrisPoints]
+        pickle.dump(len(data), f)
+        for value in data:
+            pickle.dump(value, f)
+        f.close()
+
+        print(f'{facei:5d}', end="\r")
+
+    # Remove files with failed landmark-detection.
+    # for bi, bf in zip(LandmarkFailureIndex, LandmarkFailureFile):
+    #     print("Removing " + source_files[bi])
+    #     print("     which is " + bf)
+    #     del source_files[bi]
+    #     del output_files[bi]
+    SF = np.asarray(source_files)
+    # OF = np.asarray(output_files)
+    # keep_locs = (set([l for l in range(len(output_files))]) -
+    #              set(LandmarkFailureIndex))
+    keep_locs = (set([l for l in range(len(source_files))]) -
+                 set(LandmarkFailureIndex))
+    source_files = list(SF[list(keep_locs)])
+    # output_files = list(OF[list(keep_locs)])
+
+    # Rewrite those files to disk (source directory)
+    # with open(MotherDir + 'input_files.data', 'wb') as filehandle:
+    #     pickle.dump(source_files, filehandle)
+    # with open(MotherDir + 'output_files.data', 'wb') as filehandle:
+    #     pickle.dump(output_files, filehandle)
+
+    # Create new file that lists any failures
+    # with open(MotherDir + 'excluded_files.data', 'wb') as filehandle:
+    #     pickle.dump(LandmarkFailureFile, filehandle)
+
+    # -----------------------------------------------------------------------------
+    # Produce a single JSON file that contains all landmark data
+    lmd = len(MotherDir)
+    # Combine into single dictionary
+    features = ['LEFT_EYEBROW', 'LEFT_EYE',
+                'RIGHT_EYEBROW', 'RIGHT_EYE',
+                'NOSE', 'MOUTH_OUTLINE',
+                'MOUTH_INNER', 'JAWLINE']
+    landmarks = dict()
+    number_photos = len(source_files)
+    for outfile, i in zip(source_files, range(0, number_photos)):
+        # LandmarksThisGuy = FinalLandmarks[i]
+        LandmarksThisGuy = AllSubjectsLandmarksDictAllFeature[i]
+        ThisSubjectLandmarksDict = pack_vector_xy_as_dict(LandmarksThisGuy.tolist(),
+                                                      LabelToCoordinateIndexAll)
+        fullpath = source_files[i]
+        # partpath = fullpath[fullpath.index('aligned') + len('aligned'):]
+        partpath = fullpath[lmd:]
+        this_photo = dict()
+        for fi in range(len(features)):
+            this_array = ThisSubjectLandmarksDict[features[fi] + '_POINTS']
+            # this_array = AllSubjectsLandmarksDictAllFeature[features[fi] + '_POINTS']
+            this_photo[features[fi].lower()] = \
+                list(this_array.flatten().astype(float))
+                # list(this_array.flatten().astype(np.float))
+        # TO DO
+        #   append iris points [x, y] to this_photo
+        # take from IrisPoints
+        #
+        # IrisPoints is list [p1, p2, ... pn] for n people, where
+        #   p_i is dictionary
+        #       p_i{0} = (y, x)_for right eye
+        #       p_i{1} = (y, x) for left eye
+        this_photo['left_iris'] = [float(IrisPoints[i][1][1]),
+                                   float(IrisPoints[i][1][0])]
+        this_photo['right_iris'] = [float(IrisPoints[i][0][1]),
+                                    float(IrisPoints[i][0][0])]
+        landmarks[partpath] = this_photo
+
+    # export to JSON
+    json_file = MotherDir + 'landmarks.txt'
+    with open(json_file, 'w') as outfile:
+        json.dump(landmarks, outfile)
+
+    # End of chunk for Getting Landmarks
+    #
+    # Output:
+    # source_files, output_files, AllSubjectsLandmarksDict,
+    # AllSubjectsLandmarksDictAllFeature, MeanXY, LandmarkFailureFile,
+    # LandmarkFailureIndex, IrisPoints
+    # files = []
+    # files.append(source_files)
+    # files.append(output_files)
+    if include_jaw:
+        listOfLandmarks = AllSubjectsLandmarksDictAllFeature
+    else:
+        listOfLandmarks = AllSubjectsLandmarksDict
+    print("\n\n------------------------------------------------------------\n")
+    print("\nThere should now be a JSON-formatted" +
+          "file called landmarks.txt in:\n")
+    print("\t" + MotherDir + "\n")
+    print("Please examine the contents.\n\n")
+    print("\n--------------------------------------------------------------\n")
+    return source_files, listOfLandmarks, MeanXY, IrisPoints
+    # -------------------------------------------------------------------------
+
+
+def get_landmark_features(source_dir, output_dir="", exclude_features=['jawline',
+                          'left_iris', 'right_iris', 'mouth_inner']):
+    # Returns a DICT with lots of useful stuff, like eye_distances.
+    # AllSubjectsLandmarksDict is landmarks for all faces.
+    # exclude_features refers to this; does not affect calculation of other stuff.
+
+    # Determine if landmarks.txt exists in source_dir.
+    # Load or return error if does not exist.
+    full_landmark_filename = source_dir + 'landmarks.txt'
+    exists = os.path.isfile(full_landmark_filename)
+    if exists:
+        with io.open(full_landmark_filename, 'r') as f:
+            imported_landmarks = json.loads(f.readlines()[0].strip())
+    else:
+        print(['JSON file landmarks.txt does not exist in ' + source_dir])
+        return
+
+    # Initialize results
+    eye_distances = []
+    eye_radians = []
+    eye_midpoints = []
+    mouth2eye_distances = []
+    mouth2eye_radians = []
+    nose_tips = []
+
+    # Combine source_dir and output_dir with keys of imported_landmarks to get
+    #   source_files and output_files.
+    #
+    # Also obtaining corresponding LOL as appropriate
+    #   input to alignment functions.
+    source_files = []
+    output_files = []
+    LOL = []
+    MeanXY = []
+    IrisPoints = []
+    for rest_of_file_name in imported_landmarks.keys():
+        source_files.append(source_dir + rest_of_file_name)
+        output_files.append(output_dir + rest_of_file_name)
+
+        # Convert imported_landmarks -> LOL (like listOfLandmarks)
+        dict_of_coordinates = imported_landmarks[rest_of_file_name]
+        this_person = np.array([], dtype=np.int64).reshape(0,)
+        this_iris = dict()
+
+        # Get specific features.
+        dickeys = dict_of_coordinates.keys()
+        if ('left_iris' in dickeys) and ('right_iris' in dickeys):
+            left_iris = np.array(dict_of_coordinates['left_iris'])
+            right_iris = np.array(dict_of_coordinates['right_iris'])
+        else:
+            ex = np.array(dict_of_coordinates['left_eye'][0::2]).mean()
+            ey = np.array(dict_of_coordinates['left_eye'][1::2]).mean()
+            left_iris = np.array([ex, ey])
+            ex = np.array(dict_of_coordinates['right_eye'][0::2]).mean()
+            ey = np.array(dict_of_coordinates['right_eye'][1::2]).mean()
+            right_iris = np.array([ex, ey])
+
+        mouth_inner = dict_of_coordinates['mouth_inner']
+        mouth_outline = dict_of_coordinates['mouth_outline']
+        nx = dict_of_coordinates['nose'][0::2]
+        ny = dict_of_coordinates['nose'][1::2]
+        NOSE_TIP = np.array([nx[6], ny[6]])
+        nose_tips.append(NOSE_TIP)
+
+        eye_vector = left_iris - right_iris
+        EYE_DIST = np.sqrt(((eye_vector)**2).sum())
+        EYE_RAD = np.arctan2(eye_vector[1], eye_vector[0])
+        trans_eye = np.array([(EYE_DIST / 2) * np.cos(EYE_RAD),
+                             (EYE_DIST / 2) * np.sin(EYE_RAD)])
+        EYE_MID = right_iris + trans_eye
+        eye_distances.append(EYE_DIST)
+        eye_radians.append(EYE_RAD)
+        eye_midpoints.append(EYE_MID)
+
+        mix = np.array(mouth_inner[0::2]).mean()
+        miy = np.array(mouth_inner[1::2]).mean()
+        mox = np.array(mouth_outline[0::2]).mean()
+        moy = np.array(mouth_outline[1::2]).mean()
+        mcx, mcy = (mox + mix) / 2, (moy + miy) / 2
+        mouth = np.array([mcx, mcy])
+
+        mouth_vector = mouth - EYE_MID
+        MOUTH_DIST = np.sqrt(((mouth_vector)**2).sum())
+        MOUTH_RAD = np.arctan2(mouth_vector[1], mouth_vector[0])
+        mouth2eye_distances.append(MOUTH_DIST)
+        mouth2eye_radians.append(MOUTH_RAD)
+
+        # Concatenation of landmarks (with some exclusions)
+        for this_feature in dict_of_coordinates.keys():
+            if not (this_feature in exclude_features):
+                these_coords = dict_of_coordinates[this_feature]
+                this_person = np.hstack((this_person, np.array(these_coords)))
+            if (this_feature == 'left_iris'):
+                these_coords = dict_of_coordinates[this_feature]
+                this_iris[1] = np.array([these_coords[1], these_coords[0]])
+            if (this_feature == 'right_iris'):
+                these_coords = dict_of_coordinates[this_feature]
+                this_iris[0] = np.array([these_coords[1], these_coords[0]])
+        LOL.append(this_person)
+        IrisPoints.append(this_iris)
+        xj = this_person[0::2]
+        yj = this_person[1::2]
+        MeanXY.append(np.array([int(xj.mean()), int(yj.mean())]))
+
+    AllSubjectsLandmarksDict = LOL
+
+    # Vectors of indices for each facial feature
+    for remove_this_feature in exclude_features:
+        del dict_of_coordinates[remove_this_feature]
+    CoordinateVector, LabelToCoordinateIndex = unpack_dict_to_vector_xy(dict_of_coordinates)
+
+    # Package final results.
+    landmark_features = dict()
+    landmark_features['eye_distances'] = eye_distances
+    landmark_features['eye_radians'] = eye_radians
+    landmark_features['eye_midpoints'] = eye_midpoints
+    landmark_features['mouth2eye_distances'] = mouth2eye_distances
+    landmark_features['mouth2eye_radians'] = mouth2eye_radians
+    landmark_features['nose_tips'] = nose_tips
+
+    landmark_features['AllSubjectsLandmarksDict'] = AllSubjectsLandmarksDict
+    landmark_features['IrisPoints'] = IrisPoints
+    landmark_features['MeanXY'] = MeanXY
+    landmark_features['LabelToCoordinateIndex'] = LabelToCoordinateIndex
+
+    files = []
+    files.append(source_files)
+    files.append(output_files)
+    return landmark_features, files
+
+
+def landmarks_report(source_dir, file_prefix="", file_postfix="jpg"):
+    numbers = {}
+    infiles = get_source_files(source_dir, file_prefix, file_postfix)
+    rel_paths = [fp[len(source_dir):] for fp in infiles]
+    num_total_images = len(rel_paths)
+
+    full_path_inaccurate = source_dir + "bad-landmarks.csv"
+    if os.path.isfile(full_path_inaccurate):
+        with open(full_path_inaccurate) as csv_file:
+            csv_reader = csv.reader(csv_file, delimiter=',')
+            for row in csv_reader:
+                num_detected_but_removed = len(row);
+    else:
+        num_detected_but_removed = 0;
+
+    landmark_features, files = get_landmark_features(source_dir, source_dir)
+    num_in_landmarks_file = len(files[0])
+    num_failed_detections = (num_total_images - num_in_landmarks_file -
+                             num_detected_but_removed)
+    numbers['num_total_images'] = num_total_images
+    numbers['num_detected_but_removed'] = num_detected_but_removed
+    numbers['num_failed_detections'] = num_failed_detections
+
+    print("Total input images " + str(num_total_images))
+    print("Number of images with a failed face detection " + str(num_failed_detections))
+    print("Number of images with a landmark inaccuracy " + str(num_detected_but_removed))
+
+    return numbers
+
+
+def exclude_files_with_bad_landmarks(source_dir):
+    full_bad_filename = source_dir + "bad-landmarks.csv"
+    exists = os.path.isfile(full_bad_filename)
+    if exists:
+        with open(full_bad_filename) as f:
+             reader = csv.reader(f)
+             remove_these_files = list(reader)[0]
+    else:
+        print(['CSV file bad-landmarks.csv does not exist in ' + source_dir])
+        return None
+
+    full_landmark_filename = source_dir + "landmarks.txt"
+    exists = os.path.isfile(full_landmark_filename)
+    if exists:
+        with io.open(full_landmark_filename, 'r') as f:
+            imported_landmarks = json.loads(f.readlines()[0].strip())
+    else:
+        print(['JSON file landmarks.txt does not exist in ' + source_dir])
+        return None
+
+    # First save original with a new name just in case
+    full_landmark_filename = source_dir + "landmarks-original.txt"
+    with open(full_landmark_filename, 'w') as outfile:
+        json.dump(imported_landmarks, outfile)
+
+    # Now delete unwanted entries and save as landmarks.txt
+    for this_file in remove_these_files:
+        del imported_landmarks[this_file.strip()]
+    full_landmark_filename = source_dir + "landmarks.txt"
+    with open(full_landmark_filename, 'w') as outfile:
+        json.dump(imported_landmarks, outfile)
+    return None
+
+
+def tilt_radians_to_ensure_eyes_level(the_shape, LabelToCoordinateIndex):
+    x_locs = LabelToCoordinateIndex["left_eye"][::2]
+    y_locs = LabelToCoordinateIndex["left_eye"][1::2]
+    left_center = np.array([the_shape[x_locs].mean(), the_shape[y_locs].mean()])
+    x_locs = LabelToCoordinateIndex["right_eye"][::2]
+    y_locs = LabelToCoordinateIndex["right_eye"][1::2]
+    right_center = np.array([the_shape[x_locs].mean(), the_shape[y_locs].mean()])
+    eye_vector = left_center - right_center
+    clock_wise_norm = (-eye_vector[1], eye_vector[0])
+    eye_tilt_radians = np.arctan2(clock_wise_norm[1], clock_wise_norm[0])
+    rotate_to_level_radians = np.pi / 2 - eye_tilt_radians
+    return rotate_to_level_radians
+
+
+def align_procrustes(source_dir, file_prefix='', file_postfix='jpg',
+                     exclude_features=['jawline', 'left_iris', 'right_iris',
+                     'mouth_inner'], include_features=None,
+                     adjust_size='default', size_value=None,
+                     color_of_result='grayscale'):
+    # NOTE: include_features overrides exclude_features
+
+    # files, output_dir = make_files(source_dir, file_prefix, file_postfix,
+    #                                new_dir="aligned")
+    # source_files = files[0]
+    # output_files = files[1]
+
+    output_dir = clone_directory_tree(source_dir, new_dir="aligned",
+                                      FilePrefix=file_prefix,
+                                      FilePostfix=file_postfix)
+
+    if include_features != None:
+        features = ['left_eyebrow', 'left_eye', 'right_eyebrow', 'right_eye',
+                    'nose', 'mouth_outline', 'mouth_inner', 'jawline',
+                    'left_iris', 'right_iris']
+        exclude_features = list(set(features) - set(include_features))
+
+    landmark_features, files = get_landmark_features(source_dir, output_dir,
+                                                     exclude_features)
+    source_files = files[0]
+    output_files = files[1]
+    # if len((set(source_files) - set(source_files_))) !=0:
+    #     print("source_files returned by make_files() and get_landmark_features() are different.")
+    #     print(source_files[0] + "\n" + source_files_[0])
+    #     return
+    # source_files = files[0]
+    # output_files = files[1]
+    AllSubjectsLandmarksDict = landmark_features['AllSubjectsLandmarksDict']
+    IrisPoints = landmark_features['IrisPoints']
+    MeanXY = landmark_features['MeanXY']
+
+    LabelToCoordinateIndex = landmark_features['LabelToCoordinateIndex']
+
+    # # Determine if landmarks.txt exists in source_dir.
+    # # Load or return error if does not exist.
+    # full_landmark_filename = source_dir + 'landmarks.txt'
+    # exists = os.path.isfile(full_landmark_filename)
+    # if exists:
+    #     with io.open(full_landmark_filename, 'r') as f:
+    #         imported_landmarks = json.loads(f.readlines()[0].strip())
+    # else:
+    #     print(['JSON file landmarks.txt does not exist in ' + source_dir])
+    #     return
+    #
+    # # Combine source_dir and output_dir with keys of imported_landmarks to get
+    # #   source_files and output_files.
+    # #
+    # # Also obtaining corresponding LOL as appropriate input
+    # # to alignment functions.
+    # # exclude_features = ['jawline', 'left_iris', 'right_iris']
+    # source_files = []
+    # output_files = []
+    # LOL = []
+    # MeanXY = []
+    # IrisPoints = []
+    # for rest_of_file_name in imported_landmarks.keys():
+    #     source_files.append(source_dir + rest_of_file_name)
+    #     output_files.append(output_dir + rest_of_file_name)
+    #
+    #     # Convert imported_landmarks -> LOL (like listOfLandmarks)
+    #     dict_of_coordinates = imported_landmarks[rest_of_file_name]
+    #     this_person = np.array([], dtype=np.int64).reshape(0,)
+    #     this_iris = dict()
+    #     for this_feature in dict_of_coordinates.keys():
+    #         if not (this_feature in exclude_features):
+    #             these_coords = dict_of_coordinates[this_feature]
+    #             this_person = np.hstack((this_person, np.array(these_coords)))
+    #         if (this_feature == 'left_iris'):
+    #             these_coords = dict_of_coordinates[this_feature]
+    #             this_iris[1] = (these_coords[1], these_coords[0])
+    #         if (this_feature == 'right_iris'):
+    #             these_coords = dict_of_coordinates[this_feature]
+    #             this_iris[0] = (these_coords[1], these_coords[0])
+    #     LOL.append(this_person)
+    #     IrisPoints.append(this_iris)
+    #     xj = this_person[0::2]
+    #     yj = this_person[1::2]
+    #     MeanXY.append(np.array([int(xj.mean()), int(yj.mean())]))
+    #
+    # AllSubjectsLandmarksDict = LOL
+
+    # IrisPoints is list [p1, p2, ... pn] for n people, where
+    #   p_i is dictionary
+    #       p_i{0} = (y, x)_for right eye
+    #       p_i{1} = (y, x) for left eye
+
+    # -------------------------------------------------------------------------
+    # EYE_DISTANCE, IMAGE_WIDTH, IMAGE_HEIGHT not used until 269-323
+    #   EYE_DISTANCE -> Procrustes scaling of template 269
+    #   IMAGE_WIDTH, IMAGE_HEIGHT -> padding/cropping 322-23
+    #
+    # rest of variables within are local to this section.
+    assert adjust_size in ['set_eye_distance', 'set_image_width',
+                           'set_image_height', 'default']
+    if adjust_size == 'default':
+        assert size_value is None
+
+    #  values for setting fixed proportions
+    _EYE_DISTANCE = 94
+    _IMAGE_WIDTH = 300 - 20
+    _IMAGE_HEIGHT = 338 + 80 - 30
+
+    if adjust_size == 'default':
+        EYE_DISTANCE = _EYE_DISTANCE
+        IMAGE_WIDTH = _IMAGE_WIDTH
+        IMAGE_HEIGHT = _IMAGE_HEIGHT
+    elif adjust_size == 'set_eye_distance':
+        EYE_DISTANCE = size_value
+        IMAGE_WIDTH = round((_IMAGE_WIDTH / _EYE_DISTANCE) * EYE_DISTANCE)
+        IMAGE_HEIGHT = round((_IMAGE_HEIGHT / _EYE_DISTANCE) * EYE_DISTANCE)
+    elif adjust_size == 'set_image_width':
+        IMAGE_WIDTH = size_value
+        EYE_DISTANCE = round((_EYE_DISTANCE / _IMAGE_WIDTH) * IMAGE_WIDTH)
+        IMAGE_HEIGHT = round((_IMAGE_HEIGHT / _IMAGE_WIDTH) * IMAGE_WIDTH)
+    elif adjust_size == 'set_image_height':
+        IMAGE_HEIGHT = size_value
+        EYE_DISTANCE = round((_EYE_DISTANCE / _IMAGE_HEIGHT) * IMAGE_HEIGHT)
+        IMAGE_WIDTH = round((_IMAGE_WIDTH / _IMAGE_HEIGHT) * IMAGE_HEIGHT)
+    # -------------------------------------------------------------------------
+
+    # -------------------------------------------------------------------------
+    # Get eyedist and jawdist.
+    # Need IrisPoints and AllSubjectsLandmarksDictAllFeature.
+
+    # NOTES ON ORIGINAL FORMAT OF IrisPoints
+    #
+    # IrisPoints is list [p1, p2, ... pn] for n people, where
+    #   p_i is dictionary
+    #       p_i{0} = (y, x)_for right eye
+    #       p_i{1} = (y, x) for left eye
+
+    number_so_far = len(IrisPoints)
+    # jawdist = np.empty((number_so_far, 1))
+    eyedist = np.empty((number_so_far, 1))
+    for this_face in range(0, number_so_far):
+        # lx = AllSubjectsLandmarksDictAllFeature[this_face][0::2]
+        # ly = AllSubjectsLandmarksDictAllFeature[this_face][1::2]
+        ey = [IrisPoints[this_face][0][0], IrisPoints[this_face][1][0]]
+        ex = [IrisPoints[this_face][0][1], IrisPoints[this_face][1][1]]
+        # JX = lx[0:17:16]
+        # JY = ly[0:17:16]
+        # JD = abs(np.diff(JX + JY * 1j))
+        ED = abs(np.diff(np.array(ex) + np.array(ey) * 1j))
+        # jawdist[this_face, 0] = JD[0]
+        eyedist[this_face, 0] = ED[0]
+    # -------------------------------------------------------------------------
+
+    # -------------------------------------------------------------------------
+    # Generalised Procrustes analysis
+    #
+    # Need:
+    #   AllSubjectsLandmarksDict
+    #   eyedist, EYE_DISTANCE
+    #   source_files, output_files
+    #   color_of_result
+    #   IMAGE_WIDTH, IMAGE_HEIGHT
+    #
+    # To do:
+    #   Rotate mean_shape_proper_scale by
+    #       (a) line between mouth-center and midpoint of eyes.
+    #       (b) line between eyes
+    #       (c) leave as is
+    #
+    #   Scale
+    #       (a) line between mouth-center and midpoint of eyes.
+    #       (b) line between eyes [CURRENT]
+    #
+    #   Actually, the use of specialized GP function is not necessary hereself.
+    #   I simply need the mean shape, which is simple to calculate and whose
+    #   values for each landmark are independent.
+    #
+    #   I acutally code the rest myself without specialized GP.
+    #   Check to see if that's actually correct.
+    #
+    #   True but:
+    #       new_shapes is useful for comparing with landmarks of aligned images.
+    # mean_shape, new_shapes = pt.generalized_procrustes_analysis(AllSubjectsLandmarksDict)
+    mean_shape, new_shapes, shit = generalized_procrustes_analysis(AllSubjectsLandmarksDict)
+    # pdb.set_trace()  # TEMPORARY FOR DEBUGGING
+    # # mean_shape_with_jawline, variable_not_used = pt.generalized_procrustes_analysis(AllSubjectsLandmarksDictAllFeature)
+    # mean_shape_with_jawline, shit, shat = pt.generalized_procrustes_analysis(AllSubjectsLandmarksDictAllFeature)
+    #
+    # # Set mean shape to have a head width desired for all of the faces
+    # LandmarksOfCenteredMeanShape = pack_vector_xy_as_dict(mean_shape_with_jawline.tolist(), LabelToCoordinateIndexAll)
+    # HeadWidthOfMeanShape = LandmarksOfCenteredMeanShape['JAWLINE_POINTS'][:,0].max() - LandmarksOfCenteredMeanShape['JAWLINE_POINTS'][:,0].min()
+
+
+    # LandmarksOfCenteredMeanShape = pack_vector_xy_as_dict(mean_shape.tolist(), LabelToCoordinateIndex)
+    # LE = LandmarksOfCenteredMeanShape['LEFT_EYE_POINTS'].mean(axis=0)
+    # RE = LandmarksOfCenteredMeanShape['RIGHT_EYE_POINTS'].mean(axis=0)
+    # EyeDistOfMeanShape = np.sqrt(((RE-LE)**2).sum())
+    # print([EyeDistOfMeanShape, MeanEyeDist])
+
+
+    # EYE_DISTANCE = HeadWidthConstant * EyeDistToHeadWidthRatio
+
+    # Incorrect denominator for normalization:
+    # MeanEyeDist = eyedist.mean()
+    # mean_shape_proper_scale = mean_shape * (EYE_DISTANCE / MeanEyeDist)
+    # or course, it should be the actual distance within mean_shape!!!
+
+    have_both_eyes = ("right_eye" in list(LabelToCoordinateIndex) and
+                      "left_eye" in list(LabelToCoordinateIndex))
+
+    if have_both_eyes:
+        left_eye = mean_shape[LabelToCoordinateIndex["left_eye"]]
+        right_eye = mean_shape[LabelToCoordinateIndex["right_eye"]]
+        LX = left_eye[::2].mean()
+        LY = left_eye[1::2].mean()
+        RX = right_eye[::2].mean()
+        RY = right_eye[1::2].mean()
+        mean_shape_eye_dist = np.sqrt((LX-RX)**2 + (LY-RY)**2)
+        mean_shape_proper_scale = mean_shape * (EYE_DISTANCE / mean_shape_eye_dist)
+        LabelToCoordinateIndex = landmark_features['LabelToCoordinateIndex']
+        angle_constant_rad = tilt_radians_to_ensure_eyes_level(mean_shape_proper_scale, LabelToCoordinateIndex)
+        angle_constant = angle_constant_rad * 180 / math.pi
+    else:
+        mean_shape_proper_scale = mean_shape
+        angle_constant = 0
+
+    # Now obtain precise scale and angle change for AllSubjectsLandmarksDict[i] --> mean_shape_proper_scale
+    # FinalLandmarks = []
+    # FinalLandmarksLimited = []
+    # LastLandmarkFailureFile = []
+    # LastLandmarkFailureIndex = []
+    current_working_dir = os.getcwd()
+    for infile, outfile, CenterOnThisFace in zip(source_files, output_files, range(0,len(source_files))):
+    # for infile, outfile, CenterOnThisFace in zip(source_files[0:50], output_files[0:50], range(0, 50)):
+
+        ################################
+        # from procrustes_analysis.py
+        temp_sh = np.copy(AllSubjectsLandmarksDict[CenterOnThisFace])
+        translate(temp_sh)
+
+        # get scale and rotation
+        scale, theta = get_rotation_scale(mean_shape_proper_scale, temp_sh)
+        scale = 1 / scale
+        angle_degree = (theta * 180 / math.pi) + angle_constant
+        ################################
+
+        # 0. load image to be aligned
+        # image = cv2.imread(infile)
+        image = np.array(PilImage.open(infile))
+
+        if color_of_result == 'grayscale':
+            # input_image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
+            input_image = np.array(PilImage.open(infile).convert("L"))
+        else:
+            input_image = image
+
+        # 1. translate center of landmarks to center of image
+        rows, cols = input_image.shape[0], input_image.shape[1]
+        Cy, Cx = rows/2, cols/2
+        DeltaX = Cx - MeanXY[CenterOnThisFace][0]
+        DeltaY = Cy - MeanXY[CenterOnThisFace][1]
+        # M = np.float32([[1, 0, DeltaX], [0, 1, DeltaY]])
+        # translated_image = cv2.warpAffine(input_image, M, (cols, rows))
+        tform = SimilarityTransform(translation=(-DeltaX, -DeltaY))
+        translated_image = warp(input_image, tform, preserve_range=True)
+
+        # 2. rotate to match orientation of mean shape
+        # cv_rotation_matrix = cv2.get_rotation_matrix_2d((Cx, Cy), -angle_degree, 1)
+        # rotated_image = cv2.warpAffine(translated_image,
+        #                                cv_rotation_matrix, (cols, rows))
+        angle_radians = angle_degree * np.pi / 180
+        M = get_rotation_matrix_2d((Cx, Cy), -angle_radians)
+        tform = SimilarityTransform(matrix=M)
+        rotated_image = warp(translated_image, tform, preserve_range=True).astype(np.uint8)
+
+        # 3. scale to match size of mean shape & recalculate image center
+        # scaled_image = cv2.resize(rotated_image, (0, 0), fx=scale, fy=scale)
+        oldrows, oldcols = rotated_image.shape[0], rotated_image.shape[1]
+        scaled_image = dlib.resize_image(rotated_image, int(oldrows * scale),
+                                         int(oldcols * scale))
+
+        DeltaY = EYE_DISTANCE * 5 / 12  # Can add additional options here
+        tform = SimilarityTransform(translation=(0, -DeltaY))
+        cropped_image = warp(scaled_image, tform, preserve_range=True).astype(np.uint8)
+
+        # Additional shift if mouth landmarks excluded from alignment.
+        ema = "mouth_inner" in exclude_features
+        emb = "mouth_outline" in exclude_features
+        if (ema & emb):
+            DeltaY = EYE_DISTANCE * 29 / 94
+            tform = SimilarityTransform(translation=(0, DeltaY))
+            cropped_image = warp(cropped_image, tform, preserve_range=True).astype(np.uint8)
+
+        rows, cols = cropped_image.shape[0], cropped_image.shape[1]
+        Cy, Cx = rows/2, cols/2
+
+        # 4. crop to be 256 x 256 -- centered on (Cy, Cx)
+        Cy = int(Cy)
+        Cx = int(Cx)
+        # cropped_gray = scaled_gray[Cy-128:Cy+128, Cx-128:Cx+128]
+        # cropped_gray = scaled_gray[Cy-144-15:Cy+144-15, Cx-128:Cx+128]
+        add_vertical = IMAGE_HEIGHT - cropped_image.shape[0]
+        add_horizontal = IMAGE_WIDTH - cropped_image.shape[1]
+        # if (add_vertical > 0) or (add_horizontal > 0):
+        #     pad_tuple = ((floor(add_vertical/2), ceil(add_vertical/2)), (floor(add_horizontal/2), ceil(add_horizontal/2)))
+        #     cropped_gray = np.pad(scaled_gray, pad_tuple, 'constant', constant_values=((0,0),(0,0)))
+        # else:
+        #     cropped_gray = scaled_gray
+
+        # cropped_image = scaled_image
+
+        if cropped_image.ndim == 2:
+            if (add_vertical > 0):
+                pad = ((floor(add_vertical/2), ceil(add_vertical/2)), (0, 0))
+                cropped_image = np.pad(cropped_image, pad,
+                                      'constant', constant_values=((0, 0), (0, 0)))
+            elif (add_vertical < 0):
+                pre_clip = floor(abs(add_vertical)/2)
+                pos_clip = ceil(abs(add_vertical)/2)
+                cropped_image = cropped_image[pre_clip: -pos_clip, :]
+            if (add_horizontal > 0):
+                pad = ((0, 0), (floor(add_horizontal/2), ceil(add_horizontal/2)))
+                cropped_image = np.pad(cropped_image, pad,
+                                      'constant', constant_values=((0, 0), (0, 0)))
+            elif (add_horizontal < 0):
+                pre_clip = floor(abs(add_horizontal)/2)
+                pos_clip = ceil(abs(add_horizontal)/2)
+                cropped_image = cropped_image[:, pre_clip: -pos_clip]
+        else:  # new lines to account for third channel of an RGB image
+            if (add_vertical > 0):
+                pad = ((floor(add_vertical/2), ceil(add_vertical/2)), (0, 0), (0, 0))
+                cropped_image = np.pad(cropped_image, pad,
+                                      'constant', constant_values=((0, 0), (0, 0), (0, 0)))
+            elif (add_vertical < 0):
+                pre_clip = floor(abs(add_vertical)/2)
+                pos_clip = ceil(abs(add_vertical)/2)
+                cropped_image = cropped_image[pre_clip: -pos_clip, :, :]
+            if (add_horizontal > 0):
+                pad = ((0, 0), (floor(add_horizontal/2), ceil(add_horizontal/2)), (0, 0))
+                cropped_image = np.pad(cropped_image, pad,
+                                      'constant', constant_values=((0, 0), (0, 0), (0, 0)))
+            elif (add_horizontal < 0):
+                pre_clip = floor(abs(add_horizontal)/2)
+                pos_clip = ceil(abs(add_horizontal)/2)
+                cropped_image = cropped_image[:, pre_clip: -pos_clip, :]
+
+        rows, cols = cropped_image.shape[0], cropped_image.shape[1]
+        Cy, Cx = rows/2, cols/2
+
+        # Rescale intensity to [0 255]
+        final_image = exposure.rescale_intensity(cropped_image)
+
+        DirBits = outfile.split(os.path.sep)
+        go_back = -len(DirBits[-1])
+        save_to_dir = outfile[0:go_back]
+        save_to_this = DirBits[-1]
+
+        if color_of_result == 'rgb':
+            # aligned_gray = cv2.cvtColor(final_image, cv2.COLOR_BGR2GRAY)
+            # final_image = cv2.cvtColor(final_image, cv2.COLOR_BGR2RGB)
+            aligned_gray = np.array(PilImage.fromarray(final_image).convert("L"))
+            final_image = np.array(PilImage.fromarray(final_image))
+        else:
+            aligned_gray = final_image
+
+        os.chdir(save_to_dir)
+        imsave(save_to_this, final_image)
+        os.chdir(current_working_dir)
+    print("\n\n------------------------------------------------------------\n")
+    print("\nThis directory:\n")
+    print("\t" + output_dir + "\n")
+    print("should now be populated with aligned faces.\n")
+    print("Please examine the contents.\n\n")
+    print("\n--------------------------------------------------------------\n")
+    # Write a specs.csv file to record constant image dimensions
+    fieldnames = ["adjust_size", "image_height", "image_width", "eye_distance"]
+    with open(output_dir + "specs.csv", mode="w") as csv_file:
+        writer = csv.DictWriter(csv_file, fieldnames=fieldnames)
+        writer.writeheader()
+        writer.writerow({"adjust_size": adjust_size, "image_height":IMAGE_HEIGHT, "image_width":IMAGE_WIDTH,"eye_distance":EYE_DISTANCE})
+    # return mean_shape, new_shapes, source_files
+    return output_dir
+
+
+def place_aperture(source_dir, file_prefix='', file_postfix='jpg',
+                   aperture_type="MossEgg", no_save=False, contrast_norm="max",
+                   color_of_result='grayscale'):
+    
+    source_dir = str(Path(source_dir)) + os.sep
+
+    if color_of_result == 'rgb':
+        assert (contrast_norm=="max") or (contrast_norm==None)
+
+    # files, output_dir = make_files(source_dir, file_prefix, file_postfix,
+    #                                new_dir="windowed")
+    # source_files = files[0]
+    # output_files = files[1]
+
+    output_dir = clone_directory_tree(source_dir, new_dir="windowed",
+                                      FilePrefix=file_prefix,
+                                      FilePostfix=file_postfix)
+
+    landmark_features, files = get_landmark_features(source_dir, output_dir)
+    source_files = files[0]
+    output_files = files[1]
+
+    # if len((set(source_files) - set(source_files_))) !=0:
+    #     print("source_files returned by make_files() and get_landmark_features() are different.")
+    #     print(source_files[0] + "\n" + source_files_[0])
+    #     return
+
+    shapes = np.array(landmark_features['AllSubjectsLandmarksDict'])
+    # source_files = files[0]
+    FilePostfix = source_files[0].split("/")[-1].split(".")[-1]
+
+    # Points for all faces, mean face, and center of all landmarks.
+    mean_shape = shapes.mean(axis=0)
+    MX, MY = mean_shape[0::2], mean_shape[1::2]
+    CX, CY = MX.mean(), MY.mean()
+    # size = cv2.imread(source_files[0]).shape[0:2]
+    size = np.array(PilImage.open(source_files[0]).convert("L")).shape[0:2]
+
+    aperture_good = True
+    if aperture_type == "Ellipse":
+        X = shapes[:, 0::2].reshape(-1,)
+        Y = shapes[:, 1::2].reshape(-1,)
+
+        # Longest vertical length of ellipse that fits within image.
+        if (size[0] / 2) < CY:
+            ellipse_height = (size[0] - CY) * 2
+        elif (size[0] / 2) > CY:
+            ellipse_height = CY * 2
+        else:
+            ellipse_height = size[0]
+        semi_major = ellipse_height / 2
+
+        semi_minor = fit_ellipse_semi_minor(semi_major=semi_major,
+                                            landmarks=(X, Y),
+                                            center=(CX, CY))
+
+        the_aperture = make_ellipse_map(semi_minor, semi_major,
+                                        (CX, CY), size, soften=True)
+    elif aperture_type == "MossEgg":
+        the_aperture = make_moss_egg(landmark_features, (CX, CY),
+                                     size, fraction_width=47/100, soften=True)[0]
+    else:
+        print("Error: aperture_type should be Ellipse or MossEgg.")
+        aperture_good = False
+        # the_aperture = []
+    if no_save:
+        return the_aperture
+    if aperture_good:
+        # # Need this to create all subfolders in ./in_aperture
+        # files = make_files(source_dir, FilePrefix="",
+        #                    FilePostfix=FilePostfix, new_dir="windowed")
+        # output_files = files[1]
+        if color_of_result=='grayscale':
+            for infile, outfile in zip(source_files, output_files):
+                # image = cv2.imread(infile)
+                # gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
+                gray = np.array(PilImage.open(infile).convert("L"))
+                gray = contrast_stretch(gray, inner_locs=(the_aperture * 255) > 16,
+                                        type=contrast_norm)
+                BGRA = make_four_channel_image(img=gray, aperture=the_aperture)
+
+                out_png = outfile.split(".")[0] + ".png"
+                print(outfile)
+                print(out_png)
+                # cv2.imwrite(out_png, BGRA)
+                PilImage.fromarray(BGRA).save(out_png)
+        elif color_of_result=='rgb':
+            for infile, outfile in zip(source_files, output_files):
+                # rgb = cv2.imread(infile)
+                rgb = np.array(PilImage.open(infile))
+                rgb = contrast_stretch(rgb, inner_locs=None, type=contrast_norm)
+                BGRA = make_four_channel_image(img=rgb, aperture=the_aperture)
+
+                out_png = outfile.split(".")[0] + ".png"
+                print(outfile)
+                print(out_png)
+                # cv2.imwrite(out_png, BGRA)
+                PilImage.fromarray(BGRA).save(out_png)
+        print("\n\n--------------------------------------------------------\n")
+        print("\nThere should now be a bunch of faces set in apertures in:\n")
+        print("\t" + output_dir + "\n")
+        print("Please examine the contents.\n\n")
+        print("\n----------------------------------------------------------\n")
+        return the_aperture, output_dir
+
+
+def get_mean_image(file_path, max_inner_face_contrast=False):
+    file_path = str(Path(file_path))
+    with io.open(file_path + os.sep + '/landmarks.txt', 'r') as f:
+        imported_landmarks = json.loads(f.readlines()[0].strip())
+    guys = list(imported_landmarks.keys())
+    gray_0 = np.array(PilImage.open(file_path + os.sep + guys[0]).convert("L"))
+    shape_0 = gray_0.shape
+
+    if max_inner_face_contrast:
+        # Normalize contrast within aperture, common mean of 127.5
+        # the_aperture = place_aperture(file_path, file_path, no_save=True)
+        the_aperture = place_aperture(file_path, no_save=True)
+        inner_map = (the_aperture * 255) > 16
+        gray_0 = contrast_stretch(gray_0, inner_locs=inner_map, type="mean_127") - 127.5
+    else:
+        # UINT8 to double. Center and normalize
+        gray_0 = gray_0.astype(float)
+        gray_0 -= gray_0.mean()
+        gray_0 = gray_0 / gray_0.std()
+
+    mean_image = gray_0
+    for guy in guys[1:]:
+        gray = np.array(PilImage.open(file_path + os.sep + guy).convert("L"))
+        if gray.shape==shape_0:
+
+            if max_inner_face_contrast:
+                # Normalize contrast within aperture, common mean of 127.5
+                gray = contrast_stretch(gray, inner_locs=inner_map, type="mean_127") - 127.5
+            else:
+                # UINT8 to double. Center and normalize
+                gray = gray.astype(float)
+                gray -= gray.mean()
+                gray = gray / gray.std()
+
+            mean_image += gray
+        else:
+            print("_get_mean_image() requires that all images are same dimensions!!")
+            mean_image = None
+            return mean_image
+    # print("Go back to [0-255]")
+    mean_image = mean_image / len(guys)
+    return mean_image
+
+
+def warp_to_mean_landmarks(source_dir, file_prefix='', file_postfix='jpg'):
+
+    output_dir = clone_directory_tree(source_dir, new_dir="warp-to-mean",
+                                      FilePrefix=file_prefix,
+                                      FilePostfix=file_postfix)
+
+    landmark_features, files = get_landmark_features(source_dir, output_dir,
+                                                     exclude_features=['jawline',
+                                                     'left_iris', 'right_iris'])
+    source_files = files[0]
+    L = np.array(landmark_features['AllSubjectsLandmarksDict'])
+    # source_files = files[0]
+
+    # Image size and number of images
+    # size = cv2.imread(source_files[0]).shape[0:2]
+    size = np.array(PilImage.open(source_files[0]).convert("L")).shape[0:2]
+    num_faces = len(source_files)
+
+    # Points for all faces, mean face, and center of all landmarks.
+    ML = L.mean(axis=0)
+    bx = ML[::2]
+    by = ML[1::2]
+    base = (bx, by)
+
+    # Important -> imarray and target (landmarks)
+    original_images = np.zeros((num_faces, size[0], size[1]))
+    for i, of in enumerate(source_files):
+        # image = cv2.imread(of)
+        # original_images[i, :, :] = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
+        original_images[i, :, :] = np.array(PilImage.open(of).convert("L"))
+        tx = L[i, ::2]
+        ty = L[i, 1::2]
+        target = (tx, ty)
+
+    base = np.transpose(np.array(base))
+
+    warped_to_mean = np.zeros((num_faces, size[0], size[1]))
+    for i, of in enumerate(source_files):
+        im = original_images[i, :, :]
+        im -= im.min()
+        im = im / im.max()
+
+        tx = L[i, ::2]
+        ty = L[i, 1::2]
+        target = (tx, ty)
+        target = np.transpose(np.array(target))
+
+        warpim, tri, inpix, fwdwarpix = pawarp(im, base, target,
+                                               interp='bilin')
+        warped_to_mean[i, :, :] = warpim
+
+    # Write to file
+    if not os.path.isdir(output_dir):
+        os.mkdir(output_dir)
+    for i, im in enumerate(warped_to_mean):
+        sim = (im * 255).astype("uint8")
+        out_png = output_dir + os.path.sep + "P" + str(i) + ".png"
+        # cv2.imwrite(out_png, sim)
+        PilImage.fromarray(sim).save(out_png)
+
+    # Estimate landmarks.
+    get_landmarks(output_dir, "P", "png")
+
+    # Get aperture for inner-face
+    # the_aperture = place_aperture(output_dir, output_dir, no_save=True)
+    the_aperture = place_aperture(output_dir, file_prefix='P', file_postfix='png', no_save=True)
+    inner_map = (the_aperture * 255) > 16
+
+    # Normalize contrast within aperture, common mean of 127.5
+    WTMN = np.zeros((num_faces, size[0], size[1]))
+    for i, im in enumerate(warped_to_mean):
+        nim = contrast_stretch(im, inner_locs=inner_map, type="mean_127")
+        out_png = output_dir + os.path.sep + "N" + str(i) + ".png"
+        # cv2.imwrite(out_png, nim)
+        PilImage.fromarray(nim).save(out_png)
+        WTMN[i, :, :] = nim
+
+    # Mean of warped and normalized faces, and save to file
+    AverageOfMorphs = contrast_stretch(WTMN.mean(axis=0), type="max")
+    out_png = output_dir + os.path.sep + "MEAN-N.png"
+    # cv2.imwrite(out_png, AverageOfMorphs)
+    PilImage.fromarray(AverageOfMorphs).save(out_png)
+
+    return original_images, WTMN
+
+
+def morph_between_two_faces(source_dir, do_these, num_morphs, file_prefix='',
+                            file_postfix='jpg', new_dir = "morphed",
+                            weight_texture=True):
+    assert len(do_these) == 2
+
+    output_dir = clone_directory_tree(source_dir, new_dir=new_dir,
+                                      FilePrefix=file_prefix,
+                                      FilePostfix=file_postfix)
+
+    landmark_features, files = get_landmark_features(source_dir, output_dir)
+    lms = np.array(landmark_features['AllSubjectsLandmarksDict'])
+    SF = files[0]
+
+    # select 2 faces in list do_these
+    lms = lms[do_these, :]
+    source_files = [SF[i] for i in do_these]
+
+    # Image size and number of images
+    # size = cv2.imread(source_files[0]).shape[0:2]
+    size = np.array(PilImage.open(source_files[0]).convert("L")).shape[0:2]
+    num_faces = 2
+
+    # # Points for all faces, mean face, and center of all landmarks.
+    # ML = lms.mean(axis=0)
+    # bx = ML[::2]
+    # by = ML[1::2]
+    # base = (bx, by)
+
+    original_images = np.zeros((num_faces, size[0], size[1]))
+    F, L = [], []
+    for i, of in enumerate(source_files):
+        # image = cv2.imread(of)
+        # im = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
+        im = np.array(PilImage.open(of).convert("L"))
+        im -= im.min()
+        F.append(im / im.max())
+
+        tx = lms[i, ::2]
+        ty = lms[i, 1::2]
+        target = (tx, ty)
+        L.append(np.transpose(np.array(target)))  # point by [x,y]
+
+    p = [i/(num_morphs-1) for i in range(num_morphs)]
+    face_array = np.zeros((num_morphs, F[0].shape[0], F[0].shape[1]))
+    for i in range(num_morphs):
+        N = p[i]*L[0] + (1-p[i])*L[1]
+        F0, tri, inpix, fwdwarpix = pawarp(F[0], N, L[0], interp='bilin')
+        F1, tri, inpix, fwdwarpix = pawarp(F[1], N, L[1], interp='bilin')
+        if weight_texture:
+            M = p[i]*F0 + (1-p[i])*F1
+        else:
+            M = (F0 + F1) / 2
+        face_array[i, :, :] = M
+
+    # From face A to B
+    face_array =np.flip(face_array, axis=0)
+
+    # Write to morphed faces to file
+    if not os.path.isdir(output_dir):
+        os.mkdir(output_dir)
+    for i, im in enumerate(face_array):
+        sim = (im * 255).astype("uint8")
+        out_png = output_dir + os.path.sep + "P" + str(i) + ".png"
+        # cv2.imwrite(out_png, sim)
+        PilImage.fromarray(sim).save(out_png)
+
+    # Estimate landmarks.
+    get_landmarks(output_dir, "P", "png")
+
+    # Get aperture for inner-face
+    # the_aperture = place_aperture(output_dir, output_dir, no_save=True)
+    the_aperture = place_aperture(output_dir, file_prefix='P', file_postfix='png', no_save=True)
+    inner_map = (the_aperture * 255) > 16
+
+    # Normalize contrast within aperture, common mean of 127.5
+    WTMN = np.zeros((num_morphs, size[0], size[1]))
+    for i, im in enumerate(face_array):
+        im[im>1] = 1
+        im[im<0] = 0
+        nim = contrast_stretch(im, inner_locs=inner_map, type="mean_127")
+        out_png = output_dir + os.path.sep + "N" + str(i) + ".png"
+        # cv2.imwrite(out_png, nim)
+        PilImage.fromarray(nim).save(out_png)
+        WTMN[i, :, :] = nim
+
+    return WTMN, p, output_dir
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------