adding copyright and fixing np.bool deprecation

MouseLand · Jun 13, 2023 · 9f1bb02 · 9f1bb02
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commit 9f1bb02
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Showing 41 changed files with 126 additions and 3 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 # Configuration file for the Sphinx documentation builder.
 #
 # This file only contains a selection of the most common options. For a full

diff --git a/facemap/__init__.py b/facemap/__init__.py
@@ -1 +1,4 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 name = "facemap"
diff --git a/facemap/__main__.py b/facemap/__main__.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import argparse
 import time
 from distutils.util import strtobool

diff --git a/facemap/gui/cluster.py b/facemap/gui/cluster.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 
 import cv2

diff --git a/facemap/gui/gui.py b/facemap/gui/gui.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 import sys
 from pathlib import Path

diff --git a/facemap/gui/guiparts.py b/facemap/gui/guiparts.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import numpy as np
 import pyqtgraph as pg
 from PyQt5 import QtCore, QtGui, QtWidgets

diff --git a/facemap/gui/help_windows.py b/facemap/gui/help_windows.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 
 import numpy as np

diff --git a/facemap/gui/io.py b/facemap/gui/io.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import glob
 import os
 import pickle

diff --git a/facemap/gui/menus.py b/facemap/gui/menus.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 from PyQt5.QtWidgets import QAction, QDesktopWidget
 
 from . import help_windows, io

diff --git a/facemap/keypoints.py b/facemap/keypoints.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 
 import numpy as np

diff --git a/facemap/neural_prediction/keypoints_utils.py b/facemap/neural_prediction/keypoints_utils.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 
 import numpy as np

diff --git a/facemap/neural_prediction/neural_activity.py b/facemap/neural_prediction/neural_activity.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import numpy as np
 
 from facemap import utils

diff --git a/facemap/neural_prediction/neural_model.py b/facemap/neural_prediction/neural_model.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import time
 from io import StringIO
 

diff --git a/facemap/neural_prediction/prediction_utils.py b/facemap/neural_prediction/prediction_utils.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 import time
 

diff --git a/facemap/pose/datasets.py b/facemap/pose/datasets.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 from glob import glob
 

diff --git a/facemap/pose/facemap_network.py b/facemap/pose/facemap_network.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Network ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 import numpy as np
 import torch

diff --git a/facemap/pose/model_loader.py b/facemap/pose/model_loader.py
@@ -1,4 +1,7 @@
 """
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
+"""
 Facemap model trained for generating pose estimates. Contains functions for: 
 - downloading pre-trained models
 - Model class 

diff --git a/facemap/pose/model_training.py b/facemap/pose/model_training.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 ## Import packages
 import os
 from io import StringIO

diff --git a/facemap/pose/pose.py b/facemap/pose/pose.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 import pickle
 import time

diff --git a/facemap/pose/pose_gui.py b/facemap/pose/pose_gui.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import numpy as np
 import pyqtgraph as pg
 from matplotlib import cm

diff --git a/facemap/pose/pose_helper_functions.py b/facemap/pose/pose_helper_functions.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Import packages ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 import numpy as np
 

diff --git a/facemap/pose/refine_pose.py b/facemap/pose/refine_pose.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 import shutil
 from glob import glob

diff --git a/facemap/pose/transforms.py b/facemap/pose/transforms.py
@@ -1,4 +1,7 @@
 """
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
+"""
 Facemap functions for: 
 - bounding box: (suggested ROI) for UNet input images
 - image preprocessing 

diff --git a/facemap/process.py b/facemap/process.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 import time
 from io import StringIO

diff --git a/facemap/pupil.py b/facemap/pupil.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import numpy as np
 from scipy.ndimage import gaussian_filter
 
@@ -11,7 +14,7 @@ def fit_gaussian(im, sigma=2.0, do_xy=False, missing=None):
         miss = np.isin(ix * im.shape[1] + iy, mx * im.shape[1] + my)
         miss = miss.flatten()
     else:
-        miss = np.zeros((ix.size,), np.bool)
+        miss = np.zeros((ix.size,), "bool")
 
     ix = ix[~miss].flatten()
     iy = iy[~miss].flatten()

diff --git a/facemap/roi.py b/facemap/roi.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import numpy as np
 import pyqtgraph as pg
 from PyQt5 import QtCore
@@ -94,7 +97,7 @@ def position(self, parent):
         yrange += int(sizey / 2)
         # what is ellipse circling?
         br = self.ROI.boundingRect()
-        ellipse = np.zeros((yrange.size, xrange.size), np.bool)
+        ellipse = np.zeros((yrange.size, xrange.size), "bool")
         x, y = np.meshgrid(np.arange(0, xrange.size, 1), np.arange(0, yrange.size, 1))
         ellipse = (
             (y - br.center().y()) ** 2 / (br.height() / 2) ** 2
@@ -248,7 +251,7 @@ def position(self, parent):
             yrange += int(sizey / 2)
         # what is ellipse circling?
         br = self.ROI.boundingRect()
-        ellipse = np.zeros((yrange.size, xrange.size), np.bool)
+        ellipse = np.zeros((yrange.size, xrange.size), "bool")
         x, y = np.meshgrid(np.arange(0, xrange.size, 1), np.arange(0, yrange.size, 1))
         ellipse = (
             (y - br.center().y()) ** 2 / (br.height() / 2) ** 2

diff --git a/facemap/running.py b/facemap/running.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 # outputs the dx, dy offsets between frames by registering frame N to frame
 # N-1. If the movement is larger than half the frame size, outputs NaN.
 # ops.yrange, xrange are ranges to use for rectangular section of movie

diff --git a/facemap/utils.py b/facemap/utils.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import cv2
 import h5py
 import numpy as np

diff --git a/paper/fig1.py b/paper/fig1.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import matplotlib 
 import matplotlib.pyplot as plt
 from scipy.stats import wilcoxon

diff --git a/paper/fig3.py b/paper/fig3.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import matplotlib.pyplot as plt
 import torch
 from fig_utils import *

diff --git a/paper/fig4.py b/paper/fig4.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import matplotlib.pyplot as plt
 import torch
 from fig_utils import *

diff --git a/paper/fig_utils.py b/paper/fig_utils.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import string
 
 import matplotlib

diff --git a/paper/kpsproc.py b/paper/kpsproc.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 
 import cv2

diff --git a/paper/neuralpred.py b/paper/neuralpred.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 import sys
 import time

diff --git a/paper/suppfigs.py b/paper/suppfigs.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import fig4
 import matplotlib.pyplot as plt
 import torch

diff --git a/setup.py b/setup.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import setuptools
 
 install_deps = [

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 import os
 import shutil
 import sys

diff --git a/tests/test_import.py b/tests/test_import.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 " Test imports for facemap package "
 
 

diff --git a/tests/test_neural_prediction_output.py b/tests/test_neural_prediction_output.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 " Test Facemap neural prediction output "
 
 # TODO: Add tests for neural prediction output
diff --git a/tests/test_pose_estimation_output.py b/tests/test_pose_estimation_output.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 "Test Facemap's pose estimation output "
 import os
 

diff --git a/tests/test_svd_output.py b/tests/test_svd_output.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+"""
 "Test facemap SVD processing outputs for single and multiple videos"
 import os