updated README and entry points

Author: jnj256

README.md

@@ -68,9 +68,9 @@ Before launching the interface, ensure that the Arduino board is connected to th
 
 To launch the interface, run the following command in the terminal:
 ``` bash
-python -m PhysioKit2.main --config <path of config file>
+physiokit --config <path of config file>
 see example below 
-python -m PhysioKit2.main --config configs/avr_default/sw_config.json
+physiokit --config configs/avr_default/sw_config.json
 ```
 
 This shall open user interface, basic functioning of which is shown in this demo. Please note that if secondary screen is connected, the interface uses it to adjust its resolution, however it may have to be moved to the secondary screen if it got launched on the primary.

setup.py

@@ -6,7 +6,7 @@
 long_description = (this_directory / "README.md").read_text()
 
 setup(name='PhysioKit2',
-      version='1.7.2',
+      version='1.7.3',
       description="PhysioKit: An Open-Source, Low-Cost Physiological Computing Toolkit for Single- and Multi-User Studies",
       long_description=long_description,
       long_description_content_type='text/markdown',
@@ -29,7 +29,7 @@
         'setuptools'
       ],
       packages=find_namespace_packages(where="src"),
-      package_dir={"": "src"},
+      package_dir={"": "src", 'analyze':"src/PhysioKit2/analysis_helper"},
       include_package_data=True,
       package_data={
           "PhysioKit2": ["*.txt"],
@@ -42,5 +42,11 @@
           "PhysioKit2.configs.arm_due": ["*.json"],
           "PhysioKit2.configs.avr_default": ["*.json"],
       },
-      exclude_package_data={"PhysioKit2": [".gitattributes"]}
+      exclude_package_data={"PhysioKit2": [".gitattributes"]},
+      entry_points={
+          'console_scripts': [
+              'physiokit = PhysioKit2.main:main',
+              'physiokit_analyze = PhysioKit2.analysis_helper.process_signals:main',
+          ]
+      }
       )

src/PhysioKit2/README.md

@@ -70,9 +70,9 @@ Before launching the interface, ensure that the Arduino board is connected to th
 To launch the interface, run the following command in the terminal:
 
 ``` bash
-python -m PhysioKit2.main --config <path of config file>
+physiokit --config <path of config file>
 see example below 
-python -m PhysioKit2.main --config configs/avr_default/sw_config.json
+physiokit --config configs/avr_default/sw_config.json
 ```
 
 This shall open user interface. Please note that if secondary screen is connected, the interface uses it to adjust its resolution, however it may have to be moved to the secondary screen if it got launched on the primary.

src/PhysioKit2/analysis_helper/README.md

@@ -6,7 +6,7 @@ Sample data and corresponding exp_config.json file is provided to illustrate how
 ### Step-2: Batch processing to compute metrics from PPG and EDA signals:
 
 ``` bash
-python -m PhysioKit2.analysis_helper.process_signals --config analysis_helper/exp_config.json --datapath analysis_helper sample_data --opt 0
+physiokit_analyze --config exp_config.json --datapath sample_data --opt 0
 ```
 
 ### Step-3: Saving and exporting data-tables
@@ -16,5 +16,5 @@ Following command is to illustrate the use when a specific window size and step
 Please specify the appropriate path for "analysis_dict_nk.npy" - as it would have been saved after executing the "Step-1".
 
 ``` bash
-python -m PhysioKit2.analysis_helper.process_signals --config analysis_helper/exp_config.json --datadict analysis/W120_S5__OptPPG/analysis_dict_nk.npy --opt 1
+physiokit_analyze --config exp_config.json --datadict analysis/W120_S5__OptPPG/analysis_dict_nk.npy --opt 1
 ```

src/PhysioKit2/analysis_helper/process_signals.py

@@ -1,4 +1,5 @@
 import os
+import sys
 from copy import deepcopy
 import numpy as np
 from scipy import signal
@@ -405,7 +406,7 @@ def process_data(self):
                         self.analysis_dict_nk[pid][cond] = {}
 
                         fn = os.path.join(self.datapath, pid, val["path"])
-                        _, _, ppg1, ppg2, _, _ = load_csv_data_all(fn)
+                        _, _, ppg1, ppg2, _ = load_csv_data_all(fn)
 
                         print("Processing: ", pid, cond)
                         # PPG1
@@ -629,8 +630,17 @@ def make_data_tables(self):
 
 
 
-def main(args_parser):
+def main(argv=sys.argv):
 
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--config', type=str, dest='config', help='Config file for experiment')
+    parser.add_argument('--opt', type=str, dest='opt', help='0 - process signals/  1 - make data tables', default="0")
+    parser.add_argument('--datapath', type=str, dest='datapath', help='Root directory for data', default="data")
+    parser.add_argument('--savepath', type=str, dest='savepath', help='Destination directory for saving analysis outcome', default="analysis")
+    parser.add_argument('--datadict', type=str, dest='datadict', help='Filepath for data dictionary', default="")
+    parser.add_argument('REMAIN', nargs='*')
+    args_parser = parser.parse_args()
+
     Process_Signals_obj = Process_Signals(args_parser.config, args_parser.datapath, args_parser.savepath, args_parser.datadict)
 
     if Process_Signals_obj.status:
@@ -644,15 +654,5 @@ def main(args_parser):
 
 
 if __name__ == "__main__":
-
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--config', type=str, dest='config', help='Config file for experiment')
-    parser.add_argument('--opt', type=str, dest='opt', help='0 - process signals/  1 - make data tables', default="0")
-    parser.add_argument('--datapath', type=str, dest='datapath', help='Root directory for data', default="data")
-    parser.add_argument('--savepath', type=str, dest='savepath', help='Destination directory for saving analysis outcome', default="analysis")
-    parser.add_argument('--datadict', type=str, dest='datadict', help='Filepath for data dictionary', default="")
-    parser.add_argument('REMAIN', nargs='*')
-    args_parser = parser.parse_args()
-
-    main(args_parser=args_parser)
+    main()
 

src/PhysioKit2/images/sq_indication.png

@@ -1,4 +1,5 @@
 import os
+import sys
 os.environ["PYSIDE_DESIGNER_PLUGINS"] = '.'
 os.environ["QT_LOGGING_RULES"]='*.debug=false;qt.pysideplugin=false'
 import argparse
@@ -920,18 +921,7 @@ def _draw_frame(self, framedata):
 
 
 
-def main(app, args_parser):
-    if config.OS_NAME == 'Darwin':
-        app.setStyle('Fusion')
-    
-    widget = physManager(args_parser)
-    widget.show()
-    ret = app.exec()
-
-    # sys.exit(ret)
-    return
-
-if __name__ == '__main__':
+def main(argv=sys.argv):
 
     # Create the application instance.
     app = QApplication([])
@@ -946,7 +936,21 @@ def main(app, args_parser):
     parser.add_argument('--width', default=width, dest="width", type=int)
     parser.add_argument('--height', default=height, dest="height", type=int)
 
+    # args = parser.parse_args(argv[1:])
+
     parser.add_argument('REMAIN', nargs='*')
     args_parser = parser.parse_args()
 
-    main(app, args_parser)
+
+    if config.OS_NAME == 'Darwin':
+        app.setStyle('Fusion')
+    
+    widget = physManager(args_parser)
+    widget.show()
+    ret = app.exec()
+
+    # sys.exit(ret)
+    return
+
+if __name__ == '__main__':
+    main()