add analysis cli

Author: sirfoga

.github/ISSUE_TEMPLATE/Bug_report.md

@@ -16,8 +16,15 @@ What happened instead.
 
 ## Reproduction Steps
 
-Steps to reproduce the bug
+```python
+import peeper
+
+```
 
 ## System Information
 
-OS type, model ...
+    $ python -m peeper.help
+
+```
+<paste here>
+```

peeper/analysis/cli.py

@@ -0,0 +1,61 @@
+# -*- coding: utf-8 -*-
+
+"""Command line interface"""
+
+import argparse
+import os
+
+from hal.files.models.files import Document
+from hal.streams.logger import log_message
+
+from peeper.analysis.models import Plotter
+
+
+def create_args():
+    """
+    :return: ArgumentParser
+        Parser that handles cmd arguments.
+    """
+
+    parser = argparse.ArgumentParser(usage='-i <input file> '
+                                           '-h for full usage')
+    parser.add_argument('-i', dest='file',
+                        help='input file', required=True)
+    return parser
+
+
+def parse_args(parser):
+    """
+    :param parser: ArgumentParser
+        Object that holds cmd arguments.
+    :return: tuple
+        Values of arguments.
+    """
+
+    args = parser.parse_args()
+    file = str(args.file)
+
+    assert os.path.exists(file)
+    assert Document(file).extension == ".csv"
+
+    return file
+
+
+def main():
+    file = parse_args(create_args())
+    log_message("Using file", file)
+
+    output_file = "plot.png"
+    output_file = os.path.join(os.path.dirname(file), output_file)
+
+    if os.path.exists(output_file):  # remove any previous outputs
+        os.remove(output_file)
+
+    driver = Plotter(file)
+    driver.save(output_file)
+
+    log_message("Plot saved to", output_file)
+
+
+if __name__ == '__main__':
+    main()

peeper/analysis/models.py

@@ -0,0 +1,79 @@
+# -*- coding: utf-8 -*-
+
+"""Module containing analysis models"""
+
+import pandas as pd
+from hal.files.models.files import Document
+from hal.files.models.system import ls_dir
+
+
+class Plotter:
+    """Plots data in file"""
+
+    def __init__(self, file):
+        """
+        :param file: folder where there are the input files
+        """
+
+        self.path = file
+        self.data = {
+            file: pd.read_csv(file)
+            for file in self._find_files()
+        }  # dictionary file name -> file data (as pandas data frame)
+
+    def _find_files(self):
+        """Finds files in folder
+
+        :return: list of input files in folder
+        """
+
+        files = ls_dir(self.path)
+        files = [
+            file
+            for file in files
+            if Document(file).extension == ".csv"  # just csv files
+        ]
+        return files
+
+    def _merge(self):
+        """Merges data frames into one big
+
+        :return: one big data frame with data from all input files
+        """
+
+        dfs = []  # list of data frames
+        for file, data in self.data.items():
+            file_name = Document(file).name
+            data = data.drop(["Timestamp"], axis=1)  # remove column
+            data = data.set_index("Milliseconds")  # set index
+
+            # rename columns
+            new_columns = {
+                col: file_name + " " + col
+                for col in data.keys()
+            }
+            data = data.rename(index=str, columns=new_columns)  # rename columns
+
+            dfs.append(data)
+
+        data = pd.concat(dfs, axis=1, sort=True)  # merge
+
+        # rename rows (convert to float)
+        new_rows = {
+            row: float(row)
+            for row in data.index
+        }
+        data = data.rename(index=new_rows)
+        data = data.sort_index()  # sort by index
+
+        return data
+
+    def save(self, output_file):
+        """Merges all inputs files into one
+
+        :param output_file: output file (where to write data)
+        """
+
+        data = self._merge()
+        data = sample_by_frequency(data, 5)
+        data.to_csv(output_file, index_label="Milliseconds")

peeper/preprocessing/cli.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-"""Command line interface for pre-processing models"""
+"""Command line interface"""
 
 import argparse
 import os
@@ -33,7 +33,8 @@ def parse_args(parser):
 
     args = parser.parse_args()
     directory = str(args.dir)
-    assert (os.path.exists(directory))
+
+    assert os.path.exists(directory)
 
     return directory