Revert "[WIP] Add frequency channel masking capability. Issue #125."

requirements.txt

@@ -4,7 +4,6 @@ blimpy>=2.0.0
 pandas
 toolz
 fsspec
-pyyaml
 dask
 dask[bag]
 numba

setup.py

@@ -11,7 +11,7 @@
 import numpy
 from setuptools.extension import Extension
 
-__version__ = "2.1.0"
+__version__ = "2.0.4.1"
 
 with open("README.md", "r") as fh:
     long_description = fh.read()

turbo_seti/find_doppler/data_handler.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import os
-import yaml
 import math
 import logging
 
@@ -36,8 +35,6 @@ class DATAHandle:
         Number of coarse channels.
     coarse_chans : list or None
         List of course channels.
-    mask : str, optional
-        Used to specify the frequency masking file-path.
     kernels : Kernels, optional
         Pre-configured class of Kernels.
     gpu_backend : bool, optional
@@ -47,7 +44,7 @@ class DATAHandle:
 
     """
     def __init__(self, filename=None, out_dir='./', n_coarse_chan=None, coarse_chans=None,
-                 kernels=None, gpu_backend=False, precision=2, mask=None):
+                 kernels=None, gpu_backend=False, precision=2):
         if not kernels:
             self.kernels = Kernels(gpu_backend, precision)
         else:
@@ -58,7 +55,6 @@ def __init__(self, filename=None, out_dir='./', n_coarse_chan=None, coarse_chans
             self.out_dir = out_dir
             self.n_coarse_chan = n_coarse_chan
             self.coarse_chans = coarse_chans
-            self.mask = []
 
             if not h5py.is_hdf5(filename):
                 if not sigproc.is_filterbank(filename):
@@ -83,9 +79,6 @@ def __init__(self, filename=None, out_dir='./', n_coarse_chan=None, coarse_chans
             self.header = dobj_master.header
             dobj_master.close()
 
-            # Load mask file from disk
-            self.__parse_mask_file(mask)
-
             # Split the file
             self.data_list = self.__split_h5()
             self.status = True
@@ -109,68 +102,6 @@ def get_info(self):
         fil_file = Waterfall(self.filename, load_data=False)
         return fil_file.header
 
-    def __parse_mask_file(self, mask_path):
-        r"""
-        Loads mask file from disk and creates the masking plan.
-
-        """
-        # Check if user specified a mask file
-        if not mask_path:
-            self.freq_mask = None
-            return
-
-        # Check if mask file exists and load data
-        if not os.path.isfile(mask_path):
-            error = f"Masking file ({mask_path}) not found."
-            logger.error(error)
-            raise RuntimeError(error)
-
-        with open(mask_path) as f:
-            mask_data = yaml.load(f, Loader=yaml.FullLoader)
-
-        # Verify if data from file is valid
-        if not "blacklist" in mask_data:
-            error = "Can't file blacklist key. Check mask file."
-            raise RuntimeError(error)
-
-        for r in mask_data["blacklist"]:
-            if not "range" in r:
-                error = "Invalid key inside blacklist. Check mask file."
-                raise RuntimeError(error)
-
-            start_keys = ["start"]
-            end_keys = ["end"]
-            keys = r["range"]
-
-            if len(keys) != 2:
-                error = "Invalid number of keys inside blacklist range item. Check mask file."
-                raise RuntimeError(error)
-
-            for s in keys:
-                if not any(n in s for n in (start_keys + end_keys)):
-                    error = "Invalid key inside blacklist range item. Check mask file"
-                    raise RuntimeError(error)
-
-            for a, b in [(start_keys, end_keys), (end_keys, start_keys)]:
-                for key in a:
-                    if any(key in n for n in keys) and not any(n in x for n in b for x in keys):
-                        error = f"The key `{key}` requires the `{b[0]}` key. Check mask file."
-                        raise RuntimeError(error)
-
-        def __get_by_key(d, key):
-            for k in d:
-                if key in k:
-                    return float(k[key])
-
-        # Generate mask tuple
-        for r in mask_data["blacklist"]:
-            f_start = __get_by_key(r["range"], "start")
-            f_end = __get_by_key(r["range"], "end")
-
-            self.mask.append((f_start, f_end))
-
-        print(self.mask)
-
     def __make_h5_file(self):
         r"""
         Converts file to h5 format, saved in current directory.

turbo_seti/find_doppler/find_doppler.py

@@ -56,8 +56,6 @@ class FindDoppler:
         Flags the edges of the PFF for BL data (with 3Hz res per channel).
     n_coarse_chan : int
         Number of coarse channels in file.
-    mask : str, optional
-        Used to specify the frequency masking file-path.
     kernels : Kernels, optional
         Pre-configured class of Kernels.
     gpu_backend : bool, optional
@@ -71,8 +69,8 @@ class FindDoppler:
 
     """
     def __init__(self, datafile, max_drift, min_drift=0, snr=25.0, out_dir='./', coarse_chans=None,
-                 obs_info=None, mask=None, flagging=False, n_coarse_chan=None, kernels=None,
-                 gpu_backend=False, precision=2, append_output=False, log_level_int=logging.INFO):
+                 obs_info=None, flagging=False, n_coarse_chan=None, kernels=None, gpu_backend=False,
+                 precision=2, append_output=False, log_level_int=logging.INFO):
         if not kernels:
             self.kernels = Kernels(gpu_backend, precision)
         else:
@@ -89,7 +87,6 @@ def __init__(self, datafile, max_drift, min_drift=0, snr=25.0, out_dir='./', coa
                                       out_dir=out_dir,
                                       n_coarse_chan=n_coarse_chan,
                                       coarse_chans=coarse_chans,
-                                      mask=mask,
                                       kernels=self.kernels)
         if (self.data_handle is None) or (self.data_handle.status is False):
             raise IOError("File error, aborting...")

turbo_seti/find_doppler/seti_event.py

@@ -28,8 +28,6 @@ def main(args=None):
     p.add_argument('filename', type=str, help='Name of filename to open (h5 or fil)')
     p.add_argument('-M', '--max_drift', dest='max_drift', type=float, default=10.0,
                    help='Set the drift rate to search. Unit: Hz/sec. Default: 10.0')
-    p.add_argument('-m', '--mask', dest='mask', type=str, default=None,
-                   help='Set the frequency masking file path.')
     p.add_argument('-s', '--snr', dest='snr', type=float, default=25.0,
                    help='SNR threshold. Default: 25.0')
     p.add_argument('-o', '--out_dir', dest='out_dir', type=str, default='./',
@@ -106,7 +104,6 @@ def exec(args):
                                       append_output=(args.flag_append_output == "y"),
                                       coarse_chans=coarse_chans,
                                       obs_info=None,
-                                      mask=args.mask,
                                       n_coarse_chan=args.n_coarse_chan,
                                       gpu_backend=(args.flag_gpu == "y"),
                                       precision=1 if args.flag_single_precision == "y" else 2,