From 2d50941abdd3b7fc746ed386a3bc1d6fddfdd7e0 Mon Sep 17 00:00:00 2001
From: Marina Moreira <67443181+marinagmoreira@users.noreply.github.com>
Date: Wed, 28 Feb 2024 13:42:22 -0800
Subject: [PATCH] GMM cleanup recommended by Jamie (#153)

---
 .../scripts/gmm/gmm_change_detection.py       | 24 ----------
 .../scripts/gmm/preprocess_data.py            | 45 -------------------
 .../scripts/gmm/visualization.py              | 19 ++++++++
 3 files changed, 19 insertions(+), 69 deletions(-)

diff --git a/anomaly/gmm-change-detection/scripts/gmm/gmm_change_detection.py b/anomaly/gmm-change-detection/scripts/gmm/gmm_change_detection.py
index b0e62348..6ba48346 100755
--- a/anomaly/gmm-change-detection/scripts/gmm/gmm_change_detection.py
+++ b/anomaly/gmm-change-detection/scripts/gmm/gmm_change_detection.py
@@ -47,30 +47,6 @@ def gmm_change_detection(
     n_appearances=0,
 ):
 
-    # Path to input data (.pk for pickled GMMs, PCL file,
-    # or bag files cropped to same positions at different times)
-
-    # input1 = './data/ground_truth/ground_truth_run5.pcd'
-    # input2 = './data/ground_truth/ground_truth_run4.pcd'
-
-    # input2 = "./data/single_frame_bags/20230313_1901_survey_no_bag_panorama_precut.bag"
-    # input1 = "./data/single_frame_bags/20230313_1908_survey_bag_panorama_precut.bag"
-
-    # input1 = './data/single_frame_bags/run5_astrobee.bag'
-    # input2 = './data/single_frame_bags/run1_astrobee.bag'
-
-    # input1 = './data/image_reconstruction/run5.pcd'
-    # input2 = './data/image_reconstruction/run2.pcd'
-
-    # input1 = './saved_models/fake_data_t0_1.pk'
-    # input2 = './saved_models/fake_data_t1_1.pk'
-
-    # input1 = './saved_models/20230313_1901_survey_no_bag_panorama_precut_1.pk'
-    # input2 = './saved_models/20230313_1908_survey_bag_panorama_precut_1.pk'
-
-    # input1 = 'data/image_reconstruction/run5.pcd'
-    # input2 = 'data/image_reconstruction/run4.pcd'
-
     # Get file extension
     ext = os.path.splitext(os.path.basename(input1))[1]
     current_dir = os.getcwd()
diff --git a/anomaly/gmm-change-detection/scripts/gmm/preprocess_data.py b/anomaly/gmm-change-detection/scripts/gmm/preprocess_data.py
index 02c308db..b304475d 100644
--- a/anomaly/gmm-change-detection/scripts/gmm/preprocess_data.py
+++ b/anomaly/gmm-change-detection/scripts/gmm/preprocess_data.py
@@ -48,30 +48,8 @@
 
 # See https://stackoverflow.com/questions/39772424
 def convert_pc2_pcl(data):
-
-    # # Convert the PointCloud2 message to a list of points
-    # points = list(sensor_msgs.read_points(msg, field_names=("x", "y", "z"), skip_nans=True))
-
-    # data.__class__ = sensor_msgs.msg._PointCloud2.PointCloud2
-    # offset_sorted = {f.offset: f for f in data.fields}
-    # data.fields = [f for (_, f) in sorted(offset_sorted.items())]
     # Conversion from PointCloud2 msg to np array.
     np_points = ros_numpy.point_cloud2.pointcloud2_to_xyz_array(data, remove_nans=True)
-    # np_points=np.zeros((pc.shape[0],3))
-
-    # height = pc.shape[0]
-    # if len(pc.shape) == 1:  # Unordered PC2 structure
-    #     np_points = np.zeros((height, 3), dtype=np.float32)
-    #     np_points[:, 0] = np.resize(pc["x"], height)
-    #     np_points[:, 1] = np.resize(pc["y"], height)
-    #     np_points[:, 2] = np.resize(pc["z"], height)
-
-    # else:  # Ordered PC2 structure
-    #     width = pc.shape[1]
-    #     np_points = np.zeros((height * width, 3), dtype=np.float32)
-    #     np_points[:, 0] = np.resize(pc["x"], height * width)
-    #     np_points[:, 1] = np.resize(pc["y"], height * width)
-    #     np_points[:, 2] = np.resize(pc["z"], height * width)
 
     return np_points
 
@@ -191,29 +169,6 @@ def read_pc2_msgs(bagfile):
     return merged_pcl
 
 
-# # Process data from bagfile
-# def read_pc2_msgs(bagfile):
-
-
-#     for topic, msg, t in rosbag.Bag(bagfile).read_messages():
-#         if topic == "/hw/depth_haz/extended/amplitude_int":
-#             np_im = ros_numpy.image.image_to_numpy(msg)
-#             data = Image.fromarray(np_im)
-
-#         if (
-#             topic == "/hw/depth_haz/points"
-#             or topic == "/hw/depth_haz/points/ground_truth"
-#         ):
-#             p = convert_pc2_pcl(msg)
-#             np_arr = filter_pcl(p)
-
-#             if "data" in locals():
-#                 data.show()
-#                 data.save("image.png")
-#                 return np_arr
-#     return np_arr
-
-
 # Process PCD point cloud directly
 def read_ply(pcdfile):
 
diff --git a/anomaly/gmm-change-detection/scripts/gmm/visualization.py b/anomaly/gmm-change-detection/scripts/gmm/visualization.py
index fe448f74..60bab3bc 100644
--- a/anomaly/gmm-change-detection/scripts/gmm/visualization.py
+++ b/anomaly/gmm-change-detection/scripts/gmm/visualization.py
@@ -1,3 +1,22 @@
+#!/usr/bin/env python
+# Copyright (c) 2017, United States Government, as represented by the
+# Administrator of the National Aeronautics and Space Administration.
+#
+# All rights reserved.
+#
+# The "ISAAC - Integrated System for Autonomous and Adaptive Caretaking
+# platform" software is licensed under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with the
+# License. You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
+# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
+# License for the specific language governing permissions and limitations
+# under the License.
+
 # Based on the GMM visualization code:
 #    https://github.com/sitzikbs/gmm_tutorial/blob/master/visualization.py
 # with modifications to accomodate using the model data