Rename SBAS class to Stack because for now it allows SBAS, PSI and ot…

…her analyses.

pygmtsar/pygmtsar/IO.py

@@ -17,7 +17,7 @@ class IO(datagrid):
 
     def dump(self, to_path=None):
         """
-        Dump SBAS object state to a pickle file (SBAS.pickle in the processing directory by default).
+        Dump Stack object state to a pickle file (Stack.pickle in the processing directory by default).
 
         Parameters
         ----------
@@ -31,34 +31,34 @@ def dump(self, to_path=None):
         Examples
         --------
         Dump the current state to the default dump file in the processing directory:
-        sbas.dump()
+        stack.dump()
 
         Notes
         -----
-        This method serializes the state of the SBAS object and saves it to a pickle file. The pickle file can be used to
-        restore the SBAS object with its processed data and configuration. By default, the dump file is named "SBAS.pickle"
+        This method serializes the state of the Stack object and saves it to a pickle file. The pickle file can be used to
+        restore the Stack object with its processed data and configuration. By default, the dump file is named "Stack.pickle"
         and is saved in the processing directory. An alternative file path can be provided using the `to_path` parameter.
         """
         import pickle
         import os
 
         if to_path is None:
-            sbas_pickle = os.path.join(self.basedir, 'SBAS.pickle')
+            stack_pickle = os.path.join(self.basedir, 'Stack.pickle')
         else:
             if os.path.isdir(to_path):
-                sbas_pickle = os.path.join(to_path, 'SBAS.pickle')
+                stack_pickle = os.path.join(to_path, 'Stack.pickle')
             else:
-                sbas_pickle = to_path
+                stack_pickle = to_path
 
-        print (f'NOTE: save state to file {sbas_pickle}')
-        pickle.dump(self, open(sbas_pickle, 'wb'))
+        print (f'NOTE: save state to file {stack_pickle}')
+        pickle.dump(self, open(stack_pickle, 'wb'))
 
         return
 
     @staticmethod
     def restore(from_path):
         """
-        Restore SBAS object state from a pickle file (SBAS.pickle in the processing directory by default).
+        Restore Stack object state from a pickle file (Stack.pickle in the processing directory by default).
 
         Parameters
         ----------
@@ -67,36 +67,36 @@ def restore(from_path):
 
         Returns
         -------
-        SBAS
-            The restored SBAS object.
+        Stack
+            The restored Stack object.
 
         Examples
         --------
         Restore the current state from the default dump file in the processing directory:
-        SBAS.restore()
+        Stack.restore()
 
         Notes
         -----
-        This static method restores the state of an SBAS object from a pickle file. The pickle file should contain the
-        serialized state of the SBAS object, including its processed data and configuration. By default, the method assumes
-        the input file is named "SBAS.pickle" and is located in the processing directory. An alternative file path can be
-        provided using the `from_path` parameter. The method returns the restored SBAS object.
+        This static method restores the state of an Stack object from a pickle file. The pickle file should contain the
+        serialized state of the Stack object, including its processed data and configuration. By default, the method assumes
+        the input file is named "Stack.pickle" and is located in the processing directory. An alternative file path can be
+        provided using the `from_path` parameter. The method returns the restored Stack object.
         """
         import pickle
         import os
 
         if os.path.isdir(from_path):
-            sbas_pickle = os.path.join(from_path, 'SBAS.pickle')
+            stack_pickle = os.path.join(from_path, 'Stack.pickle')
         else:
-            sbas_pickle = from_path
+            stack_pickle = from_path
 
-        print (f'NOTE: load state from file {sbas_pickle}')
-        return pickle.load(open(sbas_pickle, 'rb'))
+        print (f'NOTE: load state from file {stack_pickle}')
+        return pickle.load(open(stack_pickle, 'rb'))
 
 
     def backup(self, backup_dir, copy=False, debug=False):
         """
-        Backup framed SBAS scenes, orbits, DEM, and landmask files to build a minimal reproducible dataset.
+        Backup framed Stack scenes, orbits, DEM, and landmask files to build a minimal reproducible dataset.
 
         Parameters
         ----------
@@ -115,20 +115,20 @@ def backup(self, backup_dir, copy=False, debug=False):
         Examples
         --------
         Backup the files to the specified directory:
-        sbas.backup('backup')
+        stack.backup('backup')
 
         Open the backup for the reproducible run by defining it as a new data directory:
-        sbas = SBAS('backup', 'backup/DEM_WGS84.nc', 'raw')
+        stack = Stack('backup', 'backup/DEM_WGS84.nc', 'raw')
 
         Notes
         -----
-        This method backs up the framed SBAS scenes, orbits, DEM, and landmask files to a specified backup directory.
+        This method backs up the framed Stack scenes, orbits, DEM, and landmask files to a specified backup directory.
         It provides a way to create a minimal reproducible dataset by preserving the necessary files for processing.
         The method creates the backup directory if it does not exist. By default, the method moves the scene and orbit files
         to the backup directory, effectively removing them from the work directory. The DEM and landmask files are always
         copied to the backup directory. If the `copy` parameter is set to True, the scene and orbit files will be copied
         instead of moved. Use caution when setting `copy` to True as it can result in duplicated files and consume
-        additional storage space. The method also updates the SBAS object's dataframe to mark the removed files as empty.
+        additional storage space. The method also updates the Stack object's dataframe to mark the removed files as empty.
         """
         import os
         import shutil
@@ -137,7 +137,7 @@ def backup(self, backup_dir, copy=False, debug=False):
 
         # this optional file is dumped state, copy it if exists
         # auto-generated file can't be a symlink but user-defined symlink target should be copied
-        filename = os.path.join(self.basedir, 'SBAS.pickle')
+        filename = os.path.join(self.basedir, 'Stack.pickle')
         if os.path.exists(filename):
             if debug:
                 print ('DEBUG: copy', filename, backup_dir)
@@ -270,9 +270,9 @@ def load_pairs(self, name='phase', subswath=None):
 
     def open_grid(self, name, subswath=None, add_subswath=True, chunksize=None):
         """
-        sbas.open_grid('intf_ll2ra')
-        sbas.open_grid('intf_ra2ll')
-        sbas.open_grid('intfweight')
+        stack.open_grid('intf_ll2ra')
+        stack.open_grid('intf_ra2ll')
+        stack.open_grid('intfweight')
         """
         import xarray as xr
 
@@ -343,7 +343,7 @@ def save_grid(self, data, name, subswath=None, caption='Saving 2D grid', chunksi
 
     def open_stack(self, pairs, name, subswath=None, add_subswath=True, chunksize=None):
         """
-        sbas.open_stack(baseline_pairs,'phasefilt')
+        stack.open_stack(baseline_pairs,'phasefilt')
         """
         import xarray as xr
         import pandas as pd
@@ -437,7 +437,7 @@ def open_stack_slc(self, dates=None, subswath=None, intensity=False, dfact=2.5e-
 
     def open_stack_geotif(self, dates=None, subswath=None, intensity=False, chunksize=None):
         """
-        tiffs = sbas.open_stack_geotif(['2022-06-16', '2022-06-28'], intensity=True)
+        tiffs = stack.open_stack_geotif(['2022-06-16', '2022-06-28'], intensity=True)
         """
         import xarray as xr
         import rioxarray as rio
@@ -477,7 +477,7 @@ def open_model(self, name, chunksize=None):
         Opens an xarray 3D Dataset from a NetCDF file and re-chunks it based on the specified chunksize.
 
         This function takes the name of the model to be opened, reads the NetCDF file, and re-chunks
-        the dataset according to the provided chunksize or the default value from the 'sbas' object.
+        the dataset according to the provided chunksize or the default value from the 'stack' object.
         The 'date' dimension is always chunked with a size of 1.
 
         Parameters
@@ -486,7 +486,7 @@ def open_model(self, name, chunksize=None):
             The name of the model file to be opened.
         chunksize : int, optional
             The chunk size to be used for dimensions other than 'date'. If not provided, the default
-            chunk size from the 'sbas' object will be used.
+            chunk size from the 'stack' object will be used.
 
         Returns
         -------
@@ -537,7 +537,7 @@ def save_model(self, model, name=None, caption='Saving 3D datacube', chunksize=N
             The model to be saved.
         chunksize : int, optional
             The chunk size to be used for dimensions other than 'date'. If not provided, the default
-            chunk size from the 'sbas' object will be used.
+            chunk size from the 'stack' object will be used.
         caption: str
             The text caption for the saving progress bar.
 

pygmtsar/pygmtsar/S1.py

@@ -13,7 +13,7 @@ class S1():
     @staticmethod
     def scan_slc(datadir, orbit=None, mission=None, subswath=None, polarization=None):
         """
-        Initialize an instance of the SBAS class.
+        Initialize an instance of the Stack class.
 
         Parameters
         ----------
@@ -34,11 +34,11 @@ def scan_slc(datadir, orbit=None, mission=None, subswath=None, polarization=None
 
         Examples
         --------
-        Initialize an SBAS object with the data directory 'data' and the base directory 'raw':
-        sbas = S1('data', basedir='raw')
+        Initialize an Stack object with the data directory 'data' and the base directory 'raw':
+        stack = S1('data', basedir='raw')
 
-        Initialize an SBAS object with the data directory 'data', DEM filename 'data/DEM_WGS84.nc', and the base directory 'raw':
-        sbas = SBAS('data', 'data/DEM_WGS84.nc', 'raw')
+        Initialize an Stack object with the data directory 'data', DEM filename 'data/DEM_WGS84.nc', and the base directory 'raw':
+        stack = Stack('data', 'data/DEM_WGS84.nc', 'raw')
         """
         import os
         import shutil
@@ -217,7 +217,7 @@ def geoloc2bursts(metapath):
             raise ValueError('ERROR: Two or more scenes required')
         daily_scenes = df.groupby(['date', 'subswath'])['datetime'].count().values.max()
         if daily_scenes > 1:
-            print ('NOTE: Found multiple scenes for a single day, use function SBAS.reframe() to stitch the scenes')
+            print ('NOTE: Found multiple scenes for a single day, use function Stack.reframe() to stitch the scenes')
 
         return df
 

pygmtsar/pygmtsar/SBAS.py → pygmtsar/pygmtsar/Stack.py

@@ -7,15 +7,21 @@
 # 
 # Licensed under the BSD 3-Clause License (see LICENSE for details)
 # ----------------------------------------------------------------------------
-from .SBAS_ps import SBAS_ps
+from .Stack_ps import Stack_ps
 from .S1 import S1
 from .PRM import PRM
 
-class SBAS(SBAS_ps):
+class Stack(Stack_ps):
 
-    def __init__(self, basedir, scenes, reference=None, dem_filename=None, landmask_filename=None, drop_if_exists=False):
+    df = None
+    basedir = None
+    reference = None
+    dem_filename = None
+    landmask_filename = None
+
+    def __init__(self, basedir, drop_if_exists=False):
         """
-        Initialize an instance of the SBAS class.
+        Initialize an instance of the Stack class.
 
         Parameters
         ----------
@@ -30,11 +36,11 @@ def __init__(self, basedir, scenes, reference=None, dem_filename=None, landmask_
 
         Examples
         --------
-        Initialize an SBAS object with the data directory 'data' and the base directory 'raw':
-        sbas = SBAS('data', basedir='raw')
+        Initialize an Stack object with the data directory 'data' and the base directory 'raw':
+        stack = Stack('data', basedir='raw')
 
-        Initialize an SBAS object with the data directory 'data', DEM filename 'data/DEM_WGS84.nc', and the base directory 'raw':
-        sbas = SBAS('data', 'data/DEM_WGS84.nc', 'raw')
+        Initialize an Stack object with the data directory 'data', DEM filename 'data/DEM_WGS84.nc', and the base directory 'raw':
+        stack = Stack('data', 'data/DEM_WGS84.nc', 'raw')
         """
         import os
         import shutil
@@ -48,12 +54,12 @@ def __init__(self, basedir, scenes, reference=None, dem_filename=None, landmask_
         os.makedirs(basedir)
         self.basedir = basedir
 
+    def set_scenes(self, scenes):
         self.df = scenes
-        if reference is None:
-            print (f'NOTE: reference scene is not defined, use {scenes.index[0]}. You can change it like SBAS.set_reference("2022-01-20")')
+        if self.reference is None:
+            print (f'NOTE: auto set reference scene {scenes.index[0]}. You can change it like Stack.set_reference("2022-01-20")')
             self.reference = self.df.index[0]
-        self.set_dem(dem_filename)
-        self.set_landmask(landmask_filename)
+        return self
 
 #    def make_gaussian_filter(self, range_dec, azi_dec, wavelength, debug=False):
 #        """

pygmtsar/pygmtsar/SBAS_base.py → pygmtsar/pygmtsar/Stack_base.py

@@ -11,23 +11,23 @@
 from .tqdm_joblib import tqdm_joblib
 from .tqdm_dask import tqdm_dask
 
-class SBAS_base(tqdm_joblib, IO):
+class Stack_base(tqdm_joblib, IO):
 
     def __repr__(self):
         return 'Object %s %d items\n%r' % (self.__class__.__name__, len(self.df), self.df)
 
     def to_dataframe(self):
         """
-        Return a Pandas DataFrame for all SBAS scenes.
+        Return a Pandas DataFrame for all Stack scenes.
 
         Returns
         -------
         pandas.DataFrame
-            The DataFrame containing SBAS scenes.
+            The DataFrame containing Stack scenes.
 
         Examples
         --------
-        df = sbas.to_dataframe()
+        df = stack.to_dataframe()
         """
         return self.df
 
@@ -47,7 +47,7 @@ def multistem_stem(self, subswath, dt=None):
 
     def set_reference(self, reference):
         """
-        Define reference scene for SBAS object.
+        Define reference scene for Stack object.
 
         Parameters
         ----------
@@ -56,16 +56,16 @@ def set_reference(self, reference):
 
         Returns
         -------
-        SBAS
-            Modified instance of the SBAS class.
+        Stack
+            Modified instance of the Stack class.
 
         Examples
         --------
         Set the reference scene to '2022-01-20':
-        sbas.set_reference('2022-01-20')
+        stack.set_reference('2022-01-20')
         """
         if reference is None:
-            print ('NOTE: reference scene is None, SBAS.set_reference() command is ignored')
+            print ('NOTE: reference scene is None, Stack.set_reference() command is ignored')
             return self
         if not reference in self.df.index:
             raise Exception('Reference scene not found')
@@ -150,7 +150,7 @@ def get_subswath(self, subswath=None):
         assert subswath is None or subswath in subswaths, f'ERROR: subswath {subswath} not found'
         if subswath is not None:
             return subswath
-        assert len(subswaths)==1, f'ERROR: multiple subswaths {subswaths} found, merge them first using SBAS.merge_parallel()'
+        assert len(subswaths)==1, f'ERROR: multiple subswaths {subswaths} found, merge them first using Stack.merge_parallel()'
         # define subswath
         return subswaths[0]