bin/fits_metrics

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Created by schaffer at 12/10/19
+
+"""
+from kis_tools.interface import BasicArgParser
+from kis_tools.interface.commandline_interface import add_arg_outputfolder
+
+parser = BasicArgParser()
+add_arg_outputfolder(parser)
+
+args = parser.parse_args()
+
+from chroquest.image_metrics import calculate_and_save_metrics_for_folder
+calculate_and_save_metrics_for_folder(args.folder_in, args.folder_out)
\ No newline at end of file

chroquest/image_metrics.py

@@ -19,7 +19,7 @@ from scipy.ndimage import center_of_mass
 from tqdm import tqdm
 
 
-class ChrotelFileWrapper(ChrotelFitsFile):
+class FileWrapper(ChrotelFitsFile):
     """Simple wrapper for extracting quality metrics from a fits file"""
 
     def __init__(self, filename):
@@ -36,7 +36,6 @@ class ChrotelFileWrapper(ChrotelFitsFile):
             mean=self.data_mean(),
             max_val=self.data.max(),
             min_val=self.data.min(),
-            filter=self.FILTER,
             variance=self.data_variance(),
             center_of_mass_x=center_of_mass_x,
             center_of_mass_y=center_of_mass_y,
@@ -88,12 +87,12 @@ def get_chrotel_quality_predictors(filename):
     :param filename: path to chrotel FITS file
     :return predictors: dictionary of metric names and metric values
     """
-    cfw = ChrotelFileWrapper(filename)
+    cfw = FileWrapper(filename)
     predictors = cfw.image_quality_predictors()
     return predictors
 
 
-def calculate_and_save_metrics_for_folder(folder):
+def calculate_and_save_metrics_for_folder(folder,outpath_prefix=None):
     """
     Loop over files in folder and store all quality metrics, metrics are stored at /dat/sdc/chrotel/image_quality_data
     :param folder:
@@ -109,7 +108,7 @@ def calculate_and_save_metrics_for_folder(folder):
     for f in progress_bar:
         progress_bar.set_description(f)
         try:
-            pred = ChrotelFileWrapper(f).image_quality_predictors()
+            pred = FileWrapper(f).image_quality_predictors()
             predictors.append(pred)
         except:
             warn(f"File {f} could not be processed!")
@@ -117,8 +116,12 @@ def calculate_and_save_metrics_for_folder(folder):
 
     df = pd.DataFrame(predictors)
     df = df.set_index("filename")
-    filename = ChrotelFileWrapper(files[0]).obs_time.strftime("chrotel_quality_%Y%m%d.csv")
-    save_path = join('/dat', 'sdc', 'chrotel', 'image_quality_data', filename)
+    filename = FileWrapper(files[0]).obs_time.strftime("summary_statistics_%Y%m%d.csv")
+
+    if outpath_prefix is None:
+        save_path = join('/dat', 'sdc', 'chrotel', 'image_quality_data', filename)
+    else:
+        save_path = join(outpath_prefix,filename)
     print(f"Saving to {save_path}")
     df.to_csv(save_path)
     print(f"Saved to {save_path}")

chroquest/plots.py

@@ -16,7 +16,7 @@ from matplotlib import colors
 from matplotlib.patches import Circle
 from tqdm import tqdm
 
-from .image_metrics import ChrotelFileWrapper
+from .image_metrics import FileWrapper
 
 
 def center_of_mass_plot(df, kind='scatter'):
@@ -101,7 +101,7 @@ def ecdf_plot(data):
 
 
 def plot_chrotel(filename, ax: plt.axes):
-    f = ChrotelFileWrapper(filename)
+    f = FileWrapper(filename)
     d = f.data
     if len(d.shape) > 2:
         d = np.sum(d, axis=0)