Add basic time series module for unwrapping network inversion (#191)

* start timeseries module

* skip B for now, make vmapped versions

* start ts tests

* remove unused

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* move shapely to a test req

* start making test for ts

* make first pass at temporal avg/blockwise processor

* better test

* get basic `solve` test, add velo function

* more comments, add network invert func

* revert back tophu to not install from conda

* get test working for est velo

* revamp writers/protocols

* start setup for weighted least squares loading

* fix shapes, add weight to velo

* add spatial ref point to unw invert

* rename, more tests

* get file stack working

* [skip ci] update CHANGELOG for past releases

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/test-build-push.yml

@@ -48,6 +48,7 @@ jobs:
       - name: Install test dependencies
         run: |
           micromamba install -f tests/requirements.txt -c conda-forge
+          pip install --no-deps git+https://github.com/isce-framework/tophu@main
       - name: Enable numba boundscheck for better error catching
         run: |
           echo "NUMBA_BOUNDSCHECK=1" >> $GITHUB_ENV

CHANGELOG.md

@@ -1,4 +1,34 @@
-# [Unreleased](https://github.com/isce-framework/dolphin/compare/v0.15.0...main)
+# [Unreleased](https://github.com/isce-framework/dolphin/compare/v0.15.3...main)
+
+**Added**
+- Added `dolphin.timeseries` module with basic functionality:
+  - Invert a stack of unwrapped interferograms to a timeseries (using correlation weighting optionally)
+  - Estimate a (weighted) linear velocity from a timeseries
+- Create `DatasetStackWriter` protocol, with `BackgroundStackWriter` implementation
+
+**Changed**
+- Rename `GdalWriter` to `BackgroundBlockWriter`
+
+**Fixed**
+- `BackgroundRasterWriter`  was not creating the files necessary before writing
+
+# [0.15.3](https://github.com/isce-framework/dolphin/compare/v0.15.2...0.15.3) - 2024-02-27
+
+**Changed**
+- Return the output paths created by the ionosphere/troposphere modules to make it easier to use afterward
+
+# [0.15.2](https://github.com/isce-framework/dolphin/compare/v0.15.1...0.15.2) - 2024-02-27
+
+**Fixed**
+
+- Fixes to ionosphere/troposphere correction in for `DisplacementWorkflow` and `PsWorkflow`
+- Correct the nodata value passed through to snaphu-py
+
+# [0.15.1](https://github.com/isce-framework/dolphin/compare/v0.15.0...0.15.1) - 2024-02-26
+
+**Fixed**
+
+- PHASS now uses the Tophu wrapper to avoid isce3 inconsistencies between argument order
 
 # [0.15.0](https://github.com/isce-framework/dolphin/compare/v0.14.1...0.15.0) - 2024-02-16
 
@@ -10,7 +40,7 @@
 
 **Fixed**
 
-- Intersection of nodata regions for SLC stack are now all set to `nan` during phase linking
+- Intersection of nodata regions for SLC stack are now all set to `nan` during phase linking, avoiding 0 gaps between bursts
 
 # [0.14.1](https://github.com/isce-framework/dolphin/compare/v0.14.0...0.14.1) - 2024-02-15
 

conda-env.yml

@@ -17,7 +17,6 @@ dependencies:
   - rasterio>=1.3
   - ruamel.yaml>=0.15
   - scipy>=1.9 # "scipy 0.16+ is required for linear algebra", numba. 1.9 is the oldest version working with jax=0.4.19
-  - shapely>=1.8
   - threadpoolctl>=3.0
   - tqdm>=4.60
   - typing_extensions>=3.10

requirements.txt

@@ -9,6 +9,5 @@ pyproj>=3.3
 rasterio>=1.3
 ruamel_yaml>=0.15
 scipy>=1.9
-shapely>=1.8
 threadpoolctl>=3.0
 tqdm>=4.60

src/dolphin/io/_readers.py

@@ -28,6 +28,7 @@
 from dolphin.io._blocks import iter_blocks
 
 from ._background import _DEFAULT_TIMEOUT, BackgroundReader
+from ._utils import _ensure_slices, _unpack_3d_slices
 
 logger = logging.getLogger(__name__)
 
@@ -44,10 +45,9 @@
     "EagerLoader",
 ]
 
-if TYPE_CHECKING:
-    from builtins import ellipsis
 
-    Index = ellipsis | slice | int
+if TYPE_CHECKING:
+    from dolphin._types import Index
 
 
 @runtime_checkable
@@ -276,18 +276,6 @@ def __getitem__(self, key: tuple[Index, ...], /) -> np.ndarray:
         return _mask_array(data, self.nodata) if self.nodata is not None else data
 
 
-def _ensure_slices(rows: Index, cols: Index) -> tuple[slice, slice]:
-    def _parse(key: Index):
-        if isinstance(key, int):
-            return slice(key, key + 1)
-        elif key is ...:
-            return slice(None)
-        else:
-            return key
-
-    return _parse(rows), _parse(cols)
-
-
 @dataclass
 class RasterReader(DatasetReader):
     """A single raster band of a GDAL-compatible dataset.
@@ -414,20 +402,7 @@ def __getitem__(self, key: tuple[Index, ...], /) -> np.ndarray:
 def _read_3d(
     key: tuple[Index, ...], readers: Sequence[DatasetReader], num_threads: int = 1
 ):
-    # Check that it's a tuple of slices
-    if not isinstance(key, tuple):
-        msg = "Index must be a tuple of slices."
-        raise TypeError(msg)
-    if len(key) not in (1, 3):
-        msg = "Index must be a tuple of 1 or 3 slices."
-        raise TypeError(msg)
-    # If only the band is passed (e.g. stack[0]), convert to (0, :, :)
-    if len(key) == 1:
-        key = (key[0], slice(None), slice(None))
-    # unpack the slices
-    bands, rows, cols = key
-    # convert the rows/cols to slices
-    r_slice, c_slice = _ensure_slices(rows, cols)
+    bands, r_slice, c_slice = _unpack_3d_slices(key)
 
     if isinstance(bands, slice):
         # convert the bands to -1-indexed list

src/dolphin/io/_utils.py

@@ -0,0 +1,36 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from dolphin._types import Index
+
+
+def _ensure_slices(rows: Index, cols: Index) -> tuple[slice, slice]:
+    def _parse(key: Index):
+        if isinstance(key, int):
+            return slice(key, key + 1)
+        elif key is ...:
+            return slice(None)
+        else:
+            return key
+
+    return _parse(rows), _parse(cols)
+
+
+def _unpack_3d_slices(key: tuple[Index, ...]) -> tuple[Index, slice, slice]:
+    # Check that it's a tuple of slices
+    if not isinstance(key, tuple):
+        msg = "Index must be a tuple of slices."
+        raise TypeError(msg)
+    if len(key) not in (1, 3):
+        msg = "Index must be a tuple of 1 or 3 slices."
+        raise TypeError(msg)
+    # If only the band is passed (e.g. stack[0]), convert to (0, :, :)
+    if len(key) == 1:
+        key = (key[0], slice(None), slice(None))
+    # unpack the slices
+    bands, rows, cols = key
+    # convert the rows/cols to slices
+    r_slice, c_slice = _ensure_slices(rows, cols)
+    return bands, r_slice, c_slice