diff --git a/README.md b/README.md
index 1a3b18f4dd3885275f31c9e88e651d666ddd1a1e..8b03e447ee0dff2f2699c2a0a7e0a2096290cb8a 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,13 @@
-# chaincodes
\ No newline at end of file
+# chaincodes
+
+## Install chaincodes
+
+```bash
+pip install git+https://gitlab.lis-lab.fr/presage/chaincodes.git
+```
+
+## Transforms
+
+```python
+from chaincodes import ...
+```
diff --git a/chaincodes/chaincodes.py b/chaincodes/chaincodes.py
index e78ae8652e20181266be6b3cd26140eb65e2b618..f35aec60ef424cfebfc07f2707efc54d48476ebd 100644
--- a/chaincodes/chaincodes.py
+++ b/chaincodes/chaincodes.py
@@ -128,7 +128,7 @@ def dataframe_to_skycoords(
cdelt1 = [1] * len(feature_df)
cdelt2 = [1] * len(feature_df)
return dfp.tmap(
- lambda r: rotate_skycoord_to_map(chaincode_to_skycoord(r[0], r[1]), smap),
+ lambda r: _rotate_skycoord_to_map(chaincode_to_skycoord(r[0], r[1]), smap),
zip(
dfp.tmap(lambda r: to_chaincode(*r), zip(x, y, c, cdelt1, cdelt2)),
smaps,
@@ -136,19 +136,19 @@ def dataframe_to_skycoords(
)
-def rotate_skycoord_to_map(
+def _rotate_skycoord_to_map(
skycoord: Union[SkyCoord, List[SkyCoord]], smap: sunpy.map.Map
) -> SkyCoord:
if isinstance(skycoord, (tuple, list)):
if len(skycoord) == 0:
return []
return [
- rotate_skycoord_to_map(dfp.first(skycoord), smap)
- ] + rotate_skycoord_to_map(dfp.rest(skycoord), smap)
- return rotate_skycoord_to_time(skycoord, timestamp=smap.date)
+ _rotate_skycoord_to_map(dfp.first(skycoord), smap)
+ ] + _rotate_skycoord_to_map(dfp.rest(skycoord), smap)
+ return _rotate_skycoord_to_time(skycoord, timestamp=smap.date)
-def rotate_skycoord_to_time(
+def _rotate_skycoord_to_time(
skycoord: SkyCoord, timestamp: astropy.time.Time
) -> SkyCoord:
warnings.resetwarnings()
@@ -159,14 +159,7 @@ def rotate_skycoord_to_time(
return sk
-def project_chaincode_to_world(cc: Chaincode, smap: sunpy.map.GenericMap):
- wcs = smap.wcs
- x, y = cc.coordinates
- coords = [(x[i], y[i]) for i in range(x.shape[0])]
- return wcs.wcs_pix2world(coords, 1)
-
-
-def skycoord_to_pixel(skycoord, smap: sunpy.map.Map) -> tuple[np.ndarray, np.ndarray]:
+def _skycoord_to_pixel(skycoord, smap: sunpy.map.Map) -> tuple[np.ndarray, np.ndarray]:
y, x = skycoord.to_pixel(smap.wcs)
y = np.array(y)
x = np.array(x)
@@ -175,7 +168,7 @@ def skycoord_to_pixel(skycoord, smap: sunpy.map.Map) -> tuple[np.ndarray, np.nda
return x, y
-def complete_outline(x, y) -> tuple[np.ndarray, np.ndarray]:
+def _complete_outline(x, y) -> tuple[np.ndarray, np.ndarray]:
def interpolate(x1, y1, x2, y2):
# iterative interpolation between two integer coordinates:
# produces every integer between these two points...could be
@@ -209,15 +202,15 @@ def complete_outline(x, y) -> tuple[np.ndarray, np.ndarray]:
return out_x, out_y
-def infill_outline(outline: np.ndarray) -> np.ndarray:
+def _infill_outline(outline: np.ndarray) -> np.ndarray:
return scipy.ndimage.binary_fill_holes(outline).astype(int)
-def diff(a, which="horizontal") -> np.ndarray:
+def _diff(a, which="horizontal") -> np.ndarray:
if which == "both":
- return ((diff(a, which="horizontal") + diff(a, which="vertical")) > 0.0).astype(
- np.float64
- )
+ return (
+ (_diff(a, which="horizontal") + _diff(a, which="vertical")) > 0.0
+ ).astype(np.float64)
out = np.zeros_like(a)
for row_idx in range(1, a.shape[0]):
@@ -243,22 +236,22 @@ def chaincode_to_mask(
x, y = coord.coordinates
mask = np.zeros_like(smap.data)
mask[y.astype(int), x.astype(int)] = 1.0
- mask = infill_outline(mask)
+ mask = _infill_outline(mask)
return mask
def skycoord_to_mask(
skycoord: astropy.coordinates.SkyCoord, smap: sunpy.map.GenericMap
) -> np.ndarray:
- x, y = skycoord_to_pixel(skycoord, smap)
+ x, y = _skycoord_to_pixel(skycoord, smap)
output = np.zeros(smap.data.shape)
if x.shape[0] == 0 or y.shape[0] == 0:
return output
- x, y = complete_outline(x, y)
+ x, y = _complete_outline(x, y)
x[x >= output.shape[0]] = output.shape[0] - 1
y[y >= output.shape[1]] = output.shape[1] - 1
output[x, y] = 1.0
- output = infill_outline(output)
+ output = _infill_outline(output)
return output
@@ -282,7 +275,7 @@ def dataframe_to_mask(
return pipeline(feature_df)
-def build_chain(outline: np.ndarray) -> dict[str, Any]:
+def _build_chain(outline: np.ndarray) -> dict[str, Any]:
# generate a freeman 8 component chain code
def get_neighbours(x, y):
connected_neighbours: list[tuple[int, int]] = []
@@ -333,20 +326,20 @@ def build_chain(outline: np.ndarray) -> dict[str, Any]:
}
-def pixel_to_arcsec(
+def _pixel_to_arcsec(
x: Union[int, float], y: Union[int, float], smap: sunpy.map.GenericMap
) -> tuple[float, float]:
s = smap.pixel_to_world(x * u.pixel, y * u.pixel)
return s.Tx.value, s.Ty.value
-def mask_to_chaincode(mask: np.ndarray, smap: sunpy.map.Map) -> pd.DataFrame:
+def mask_to_dataframe(mask: np.ndarray, smap: sunpy.map.Map) -> pd.DataFrame:
chaincodes: list[dict[str, Any]] = []
labelled_array, n_features = scipy.ndimage.label(mask)
for feature_idx in range(1, n_features + 1):
_tmp = labelled_array == feature_idx
- outline = diff((_tmp == 1).astype(np.int8), "both")
- code = build_chain(outline)
+ outline = _diff((_tmp == 1).astype(np.int8), "both")
+ code = _build_chain(outline)
chaincodes.append(code)
df = pd.DataFrame(chaincodes)
df["cdelt1"] = smap.meta["cdelt1"]
@@ -355,7 +348,7 @@ def mask_to_chaincode(mask: np.ndarray, smap: sunpy.map.Map) -> pd.DataFrame:
df["cc_y_arcsec"] = 0.0
for row_idx in range(df.shape[0]):
x, y = df.loc[row_idx, "cc_x_pix"], df.loc[row_idx, "cc_y_pix"]
- x, y = pixel_to_arcsec(x, y, smap)
+ x, y = _pixel_to_arcsec(x, y, smap)
df.loc[row_idx, "cc_x_arcsec"] = x
df.loc[row_idx, "cc_y_arcsec"] = y
df["date_obs"] = smap.date.strftime("%Y-%m-%dT%H:%M:%S") # isoformat