impdar - npm Package Compare versions

Comparing version 1.2.0 to 1.2.1

PKG-INFO

@@ -1,4 +0,4 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: impdar
-Version: 1.2.0
+Version: 1.2.1
 Summary: Scripts for impulse radar
@@ -15,2 +15,3 @@ Author-email: David Lilien <[e-mail]>
 Requires-Dist: segyio
+Dynamic: license-file
 
@@ -17,0 +18,0 @@ # ImpDAR: an impulse radar processor

pyproject.toml

 [project]
 name = "impdar"
-version = "1.2.0"
+version = "1.2.1"
 description = "Scripts for impulse radar"
@@ -5,0 +5,0 @@ readme = "README.md"

src/impdar.egg-info/PKG-INFO

@@ -1,4 +0,4 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: impdar
-Version: 1.2.0
+Version: 1.2.1
 Summary: Scripts for impulse radar
@@ -15,2 +15,3 @@ Author-email: David Lilien <[e-mail]>
 Requires-Dist: segyio
+Dynamic: license-file
 
@@ -17,0 +18,0 @@ # ImpDAR: an impulse radar processor

src/impdar/bin/impdarexec.py

@@ -28,3 +28,3 @@ #! /usr/bin/env python
                              help='File(s) to load')
-    parser_load.add_argument('-channel', type=int, default=1,
+    parser_load.add_argument('-channel', type=str, default="processed",
                              help='Receiver channel to load this is primarily for the St. Olaf HF data.')
@@ -31,0 +31,0 @@ parser_load.add_argument('-gps_offset',

src/impdar/lib/ApresData/ApresFlags.py

@@ -67,3 +67,3 @@ #! /usr/bin/env python
         """
-        outmat = {att: (getattr(self, att) if getattr(self, att) is not None else np.NaN) for att in self.attrs}
+        outmat = {att: (getattr(self, att) if getattr(self, att) is not None else np.nan) for att in self.attrs}
         return outmat
@@ -137,3 +137,3 @@
         """
-        outmat = {att: (getattr(self, att) if getattr(self, att) is not None else np.NaN) for att in self.attrs}
+        outmat = {att: (getattr(self, att) if getattr(self, att) is not None else np.nan) for att in self.attrs}
         return outmat
@@ -140,0 +140,0 @@

src/impdar/lib/gpslib.py

@@ -68,4 +68,8 @@ #! /usr/bin/env python
         out_cs = osr.SpatialReference()
-        out_cs.SetFromUserInput(t_srs)
         try:
+            out_cs.SetFromUserInput(t_srs)
+        except TypeError:
+            out_cs.SetFromUserInput(t_srs[0])
+
+        try:
             out_cs.SetAxisMappingStrategy(osr.OAMS_TRADITIONAL_GIS_ORDER)
@@ -386,3 +390,3 @@ except AttributeError:
     else:
-        fill_value = np.NaN
+        fill_value = np.nan
 
@@ -389,0 +393,0 @@ if type(dats) not in [list, tuple]:

src/impdar/lib/load/__init__.py

@@ -126,3 +126,3 @@ #! /usr/bin/env python
                 for fn in fns_in:
-                    dat += load_UoA.load_UoA_h5(fn, gps_offset=gps_offset)
+                    dat += load_UoA.load_UoA_h5(fn, gps_offset=gps_offset, channel=channel)
         else:
@@ -129,0 +129,0 @@ raise ImportError('You need h5py for UoA')

src/impdar/lib/load/load_bsi.py

@@ -79,4 +79,3 @@ #! /usr/bin/env python
             h5_data.tnum = len(list(dset.keys()))
-            h5_data.snum = len(
-                dset['location_0']['datacapture_0']['echogram_0'])
+            h5_data.snum = len(dset['location_0']['datacapture_0']['echogram_0'])
             lat = np.zeros((h5_data.tnum,))
@@ -115,3 +114,3 @@ lon = np.zeros((h5_data.tnum,))
 
-            if type(dset['location_0']['datacapture_'+ch]['echogram_'+ch].attrs[dig_meta_str]) == str:
+            if type(dset['location_0']['datacapture_'+ch]['echogram_'+ch].attrs[dig_meta_str]) is str:
                 digitizer_data = dset['location_0']['datacapture_'+ch][
@@ -128,3 +127,3 @@ 'echogram_'+ch].attrs[dig_meta_str]
                     h5_data.snum = nsamps
-                h5_data.data[:, location_num] = dset[
+                h5_data.data[:nsamps, location_num] = dset[
                     'location_{:d}'.format(location_num)][
@@ -134,3 +133,3 @@ 'datacapture_'+ch]['echogram_'+ch]
                     'datacapture_'+ch]['echogram_'+ch].attrs[
-                        gps_cluster_str]) == str:
+                        gps_cluster_str]) is str:
                     gps_data = dset['location_{:d}'.format(location_num)][
@@ -157,4 +156,10 @@ 'datacapture_'+ch]['echogram_'+ch].attrs[
                         lon[location_num] = np.nan
-                    time[location_num] = float(_xmlGetVal(gps_data, gps_timestamp_str))
-                    h5_data.elev[location_num] = float(_xmlGetVal(gps_data, alt_asl))
+                    try:
+                        time[location_num] = float(_xmlGetVal(gps_data, gps_timestamp_str))
+                    except ValueError:
+                        time[location_num] = np.nan
+                    try:
+                        h5_data.elev[location_num] = float(_xmlGetVal(gps_data, alt_asl))
+                    except ValueError:
+                        h5_data.elev[location_num] = np.nan
                 else:
@@ -161,0 +166,0 @@ lat[location_num] = np.nan

src/impdar/lib/load/load_pulse_ekko.py

@@ -39,3 +39,3 @@ #! /usr/bin/env python
         self.bytes_per_point = np.zeros((1, tnum))
-        self.n_stackes = np.zeros((1, tnum))
+        self.n_stacks = np.zeros((1, tnum))
         self.time_window = np.zeros((1, tnum))
@@ -61,3 +61,3 @@ self.pos = np.zeros((3, tnum))
         self.bytes_per_point[0, self.header_index] = header[5]
-        self.n_stackes[0, self.header_index] = header[7]
+        self.n_stacks[0, self.header_index] = header[7]
         self.time_window[0, self.header_index] = header[8]
@@ -177,6 +177,5 @@ self.pos[0, self.header_index] = header[9]
     try:
-        strtypes = (unicode, str)
+        unicode
         openmode_unicode = 'rU'
     except NameError:
-        strtypes = (str, )
         openmode_unicode = 'r'
@@ -194,3 +193,2 @@
         fin.seek(0)
-        print(pe_data.version)
         for i, line in enumerate(fin):
@@ -211,7 +209,13 @@ if 'TRACES' in line or 'NUMBER OF TRACES' in line:
                     doy = (int(line[:4]), int(line[5:7]), int(line[8:10]))
-            if i == 2 and pe_data.version != '1.0':
-                doy = (int(line[6:10]), int(line[:2]), int(line[3:5]))
+                day_offset = datetime.datetime(doy[0], doy[1], doy[2], 0, 0, 0)
+            elif i == 2 and float(pe_data.version) <= 1.5:
+                try:
+                    doy = (int(line[6:10]), int(line[:2]), int(line[3:5]))
+                except ValueError:
+                    doy = (int(line[28:32]), int(line[34:36]), int(line[36:38]))
+                day_offset = datetime.datetime(doy[0], doy[1], doy[2], 0, 0, 0)
+            elif i == 2 and float(pe_data.version) > 1.5:
+                fmt = "%Y-%b-%d\nT%H:%M:%S"
+                day_offset = datetime.datetime.strptime(line + "T00:00:00", fmt)
 
-        day_offset = datetime.datetime(doy[0], doy[1], doy[2], 0, 0, 0)
-
     if pe_data.version == '1.0':
@@ -218,0 +222,0 @@ pe_data.data = np.zeros((pe_data.snum, pe_data.tnum), dtype=np.int16)

src/impdar/lib/load/load_UoA.py

@@ -86,3 +86,3 @@ #! /usr/bin/env python
 
-def load_UoA_h5(fn, gps_offset=0.0):
+def load_UoA_h5(fn, gps_offset=0.0, channel="processed"):
     """Load MCoRDS data in .mat format downloaded from the CReSIS ftp client
@@ -99,3 +99,3 @@
             raise ValueError('Can only unpack MultiChannel UoA data')
-        if 'processed' in fin:
+        if channel == "processed" and 'processed' in fin:
             for name in fin['processed'].keys():
@@ -109,17 +109,28 @@ for integrator in fin['processed'][name].keys():
                     data_list.append(UoA_data)
-
         else:
-            print('No processed data found, reading channels')
-            for i in range(8):
-                if f'channel_{i}' in fin:
-                    for integrator in fin[f'channel_{i}'].keys():
-                        grp = fin[f'channel_{i}'][integrator]
-                        UoA_data = RadarData(None)
-                        UoA_data.fn = fn[:-3] + f'_ch{i}_Int' + integrator[-1]
+            if f'channel_{channel}' in fin:
+                for integrator in fin[f'channel_{channel}'].keys():
+                    grp = fin[f'channel_{channel}'][integrator]
+                    UoA_data = RadarData(None)
+                    UoA_data.fn = fn[:-3] + f'_ch{channel}_Int' + integrator[-1]
 
-                        UoA_data.chan = i
-                        _load_group(UoA_data, grp, gps_offset)
+                    UoA_data.chan = channel
+                    _load_group(UoA_data, grp, gps_offset)
 
-                        data_list.append(UoA_data)
+                    data_list.append(UoA_data)
 
+            else:
+                print('No processed data found, reading channels')
+                for i in range(8):
+                    if f'channel_{i}' in fin:
+                        for integrator in fin[f'channel_{i}'].keys():
+                            grp = fin[f'channel_{i}'][integrator]
+                            UoA_data = RadarData(None)
+                            UoA_data.fn = fn[:-3] + f'_ch{i}_Int' + integrator[-1]
+
+                            UoA_data.chan = i
+                            _load_group(UoA_data, grp, gps_offset)
+
+                            data_list.append(UoA_data)
+
     return data_list
@@ -148,5 +159,3 @@
         nminfo.elev = np.zeros_like(nminfo.lat)
-        print(nminfo.lat.shape)
-        print(nminfo.lon.shape)
-        print(nminfo.elev.shape)
+        print(nminfo.lat.shape, UoA_data.data.shape[1])
 
@@ -153,0 +162,0 @@ if nminfo.lat.shape[0] > UoA_data.tnum:

src/impdar/lib/process.py

@@ -252,3 +252,3 @@ #! /usr/bin/env python
         for attr in pick_attrs:
-            setattr(out.picks, attr, np.zeros((len(all_picks), out.tnum)) * np.NaN)
+            setattr(out.picks, attr, np.zeros((len(all_picks), out.tnum)) * np.nan)
         start_ind = 0
@@ -255,0 +255,0 @@ for dat in radar_data:

src/impdar/lib/RadarData/__init__.py

@@ -344,2 +344,4 @@ #! /usr/bin/env python
             transform, self.t_srs = gpslib.get_conversion(t_srs=t_srs)
+        elif self.t_srs is not None:
+            transform, _ = gpslib.get_conversion(t_srs=self.t_srs)
         else:
@@ -346,0 +348,0 @@ transform, self.t_srs = gpslib.get_utm_conversion(np.nanmean(self.lat), np.nanmean(self.long))

test/test_ApresFlags.py

@@ -13,5 +13,3 @@ #! /usr/bin/env python
 
-import os
 import unittest
-import numpy as np
 from impdar.lib.ApresData import ApresFlags, TimeDiffFlags, QuadPolFlags
@@ -18,0 +16,0 @@

test/test_gpslib.py

@@ -91,3 +91,3 @@ #! /usr/bin/env python
         dat = NoInitRadarData(big=True)
-        dat.decday[10] = np.NaN
+        dat.decday[10] = np.nan
 
@@ -94,0 +94,0 @@ gpslib.kinematic_gps_control(dat, np.arange(0, 2.0, 0.1), np.arange(40, 60, 1), np.arange(0, 2000, 100), np.arange(0, 20, 1), guess_offset=False)

test/test_picklib.py

@@ -135,5 +135,5 @@ #! /usr/bin/env python
 
-        thatdata.picks.samp1[:, :] = np.NaN
-        thatdata.picks.samp2[:, :] = np.NaN
-        thatdata.picks.samp3[:, :] = np.NaN
+        thatdata.picks.samp1[:, :] = np.nan
+        thatdata.picks.samp2[:, :] = np.nan
+        thatdata.picks.samp3[:, :] = np.nan
         tnum, sn = picklib.get_intersection(thisdata, thatdata, multiple_int=False, return_nans=True)
@@ -140,0 +140,0 @@ self.assertTrue(len(sn) == len(thisdata.picks.picknums))

test/test_Picks.py

@@ -71,3 +71,3 @@ #! /usr/bin/env python
     def test_smooth(self):
-        # first, no NaNs
+        # first, no nans
         data = RadarData(os.path.join(THIS_DIR, 'input_data', 'small_data_picks.mat'))
@@ -81,8 +81,8 @@ cache_val = data.picks.samp1.copy()
 
-        # NaNs ends only
+        # nans ends only
         data = RadarData(os.path.join(THIS_DIR, 'input_data', 'small_data_picks.mat'))
         for attr in ['samp1', 'samp2', 'samp3', 'power']:
             val = getattr(data.picks, attr)
-            val[:, -1] = np.NaN
-            val[:, 0] = np.NaN
+            val[:, -1] = np.nan
+            val[:, 0] = np.nan
             setattr(data.picks, attr, val)
@@ -95,5 +95,5 @@ data.picks.smooth(4, units='tnum')
             val = getattr(data.picks, attr)
-            val[:, -1] = np.NaN
-            val[:, 0] = np.NaN
-            val[:, 5] = np.NaN
+            val[:, -1] = np.nan
+            val[:, 0] = np.nan
+            val[:, 5] = np.nan
             setattr(data.picks, attr, val)
@@ -106,3 +106,3 @@ data.picks.smooth(4, units='tnum')
             val = getattr(data.picks, attr)
-            val[0, :] = np.NaN
+            val[0, :] = np.nan
             setattr(data.picks, attr, val)
@@ -116,5 +116,5 @@ data.picks.smooth(4, units='tnum')
             val = getattr(data.picks, attr)
-            val[:, -1] = np.NaN
-            val[:, 0] = np.NaN
-            val[:, 5] = np.NaN
+            val[:, -1] = np.nan
+            val[:, 0] = np.nan
+            val[:, 5] = np.nan
             setattr(data.picks, attr, val)
@@ -121,0 +121,0 @@ data.picks.smooth(4, units='dist')

test/test_plot.py

@@ -286,3 +286,3 @@ #! /usr/bin/env python
 
-        dat.picks.samp2[:, 1] = np.NaN  # make sure no bugs if this is at the bottom
+        dat.picks.samp2[:, 1] = np.nan  # make sure no bugs if this is at the bottom
         fig, ax = plot.plot_radargram(dat, flatten_layer=10)
@@ -289,0 +289,0 @@

test/test_RadarDataSaving.py

@@ -155,3 +155,3 @@ #! /usr/bin/env python
 
-        # First, export with NaNs, both with normal field (depth) and elev
+        # First, export with nans, both with normal field (depth) and elev
         rd.picks.samp2[:] = np.nan
@@ -169,3 +169,3 @@ with warnings.catch_warnings(record=True) as w:
 
-        # Fill in NaNs
+        # Fill in nans
         rd.picks.samp2[:] = 1
@@ -204,3 +204,3 @@ with warnings.catch_warnings(record=True) as w:
 
-        # First, export with NaNs
+        # First, export with nans
         rd.picks.samp2[:] = np.nan
@@ -220,3 +220,3 @@ rd.output_csv(os.path.join(THIS_DIR, 'input_data', 'test.csv'))
 
-        # Fill in NaNs
+        # Fill in nans
         rd.picks.samp2[:] = 1
@@ -223,0 +223,0 @@ rd.output_csv(os.path.join(THIS_DIR, 'input_data', 'test.csv'))

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