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astropy/astropy | astropy__astropy-12907 | d16bfe05a744909de4b27f5875fe0d4ed41ce607 | diff --git a/astropy/modeling/separable.py b/astropy/modeling/separable.py
--- a/astropy/modeling/separable.py
+++ b/astropy/modeling/separable.py
@@ -242,7 +242,7 @@ def _cstack(left, right):
cright = _coord_matrix(right, 'right', noutp)
else:
cright = np.zeros((noutp, right.shape[1]))
- cright[-right.shape[0]:, -right.shape[1]:] = 1
+ cright[-right.shape[0]:, -right.shape[1]:] = right
return np.hstack([cleft, cright])
| diff --git a/astropy/modeling/tests/test_separable.py b/astropy/modeling/tests/test_separable.py
--- a/astropy/modeling/tests/test_separable.py
+++ b/astropy/modeling/tests/test_separable.py
@@ -28,6 +28,13 @@
p1 = models.Polynomial1D(1, name='p1')
+cm_4d_expected = (np.array([False, False, True, True]),
+ np.array([[True, True, False, False],
+ [True, True, False, False],
+ [False, False, True, False],
+ [False, False, False, True]]))
+
+
compound_models = {
'cm1': (map3 & sh1 | rot & sh1 | sh1 & sh2 & sh1,
(np.array([False, False, True]),
@@ -52,7 +59,17 @@
'cm7': (map2 | p2 & sh1,
(np.array([False, True]),
np.array([[True, False], [False, True]]))
- )
+ ),
+ 'cm8': (rot & (sh1 & sh2), cm_4d_expected),
+ 'cm9': (rot & sh1 & sh2, cm_4d_expected),
+ 'cm10': ((rot & sh1) & sh2, cm_4d_expected),
+ 'cm11': (rot & sh1 & (scl1 & scl2),
+ (np.array([False, False, True, True, True]),
+ np.array([[True, True, False, False, False],
+ [True, True, False, False, False],
+ [False, False, True, False, False],
+ [False, False, False, True, False],
+ [False, False, False, False, True]]))),
}
| Modeling's `separability_matrix` does not compute separability correctly for nested CompoundModels
Consider the following model:
```python
from astropy.modeling import models as m
from astropy.modeling.separable import separability_matrix
cm = m.Linear1D(10) & m.Linear1D(5)
```
It's separability matrix as you might expect is a diagonal:
```python
>>> separability_matrix(cm)
array([[ True, False],
[False, True]])
```
If I make the model more complex:
```python
>>> separability_matrix(m.Pix2Sky_TAN() & m.Linear1D(10) & m.Linear1D(5))
array([[ True, True, False, False],
[ True, True, False, False],
[False, False, True, False],
[False, False, False, True]])
```
The output matrix is again, as expected, the outputs and inputs to the linear models are separable and independent of each other.
If however, I nest these compound models:
```python
>>> separability_matrix(m.Pix2Sky_TAN() & cm)
array([[ True, True, False, False],
[ True, True, False, False],
[False, False, True, True],
[False, False, True, True]])
```
Suddenly the inputs and outputs are no longer separable?
This feels like a bug to me, but I might be missing something?
| 2022-03-03T15:14:54Z | 4.3 | ["astropy/modeling/tests/test_separable.py::test_separable[compound_model6-result6]", "astropy/modeling/tests/test_separable.py::test_separable[compound_model9-result9]"] | ["astropy/modeling/tests/test_separable.py::test_coord_matrix", "astropy/modeling/tests/test_separable.py::test_cdot", "astropy/modeling/tests/test_separable.py::test_cstack", "astropy/modeling/tests/test_separable.py::test_arith_oper", "astropy/modeling/tests/test_separable.py::test_separable[compound_model0-result0]", "astropy/modeling/tests/test_separable.py::test_separable[compound_model1-result1]", "astropy/modeling/tests/test_separable.py::test_separable[compound_model2-result2]", "astropy/modeling/tests/test_separable.py::test_separable[compound_model3-result3]", "astropy/modeling/tests/test_separable.py::test_separable[compound_model4-result4]", "astropy/modeling/tests/test_separable.py::test_separable[compound_model5-result5]", "astropy/modeling/tests/test_separable.py::test_separable[compound_model7-result7]", "astropy/modeling/tests/test_separable.py::test_separable[compound_model8-result8]", "astropy/modeling/tests/test_separable.py::test_custom_model_separable"] | 298ccb478e6bf092953bca67a3d29dc6c35f6752 |
|
astropy/astropy | astropy__astropy-14182 | a5917978be39d13cd90b517e1de4e7a539ffaa48 | diff --git a/astropy/io/ascii/rst.py b/astropy/io/ascii/rst.py
--- a/astropy/io/ascii/rst.py
+++ b/astropy/io/ascii/rst.py
@@ -27,7 +27,6 @@ def get_fixedwidth_params(self, line):
class SimpleRSTData(FixedWidthData):
- start_line = 3
end_line = -1
splitter_class = FixedWidthTwoLineDataSplitter
@@ -39,12 +38,29 @@ class RST(FixedWidth):
Example::
- ==== ===== ======
- Col1 Col2 Col3
- ==== ===== ======
- 1 2.3 Hello
- 2 4.5 Worlds
- ==== ===== ======
+ >>> from astropy.table import QTable
+ >>> import astropy.units as u
+ >>> import sys
+ >>> tbl = QTable({"wave": [350, 950] * u.nm, "response": [0.7, 1.2] * u.count})
+ >>> tbl.write(sys.stdout, format="ascii.rst")
+ ===== ========
+ wave response
+ ===== ========
+ 350.0 0.7
+ 950.0 1.2
+ ===== ========
+
+ Like other fixed-width formats, when writing a table you can provide ``header_rows``
+ to specify a list of table rows to output as the header. For example::
+
+ >>> tbl.write(sys.stdout, format="ascii.rst", header_rows=['name', 'unit'])
+ ===== ========
+ wave response
+ nm ct
+ ===== ========
+ 350.0 0.7
+ 950.0 1.2
+ ===== ========
Currently there is no support for reading tables which utilize continuation lines,
or for ones which define column spans through the use of an additional
@@ -57,10 +73,15 @@ class RST(FixedWidth):
data_class = SimpleRSTData
header_class = SimpleRSTHeader
- def __init__(self):
- super().__init__(delimiter_pad=None, bookend=False)
+ def __init__(self, header_rows=None):
+ super().__init__(delimiter_pad=None, bookend=False, header_rows=header_rows)
def write(self, lines):
lines = super().write(lines)
- lines = [lines[1]] + lines + [lines[1]]
+ idx = len(self.header.header_rows)
+ lines = [lines[idx]] + lines + [lines[idx]]
return lines
+
+ def read(self, table):
+ self.data.start_line = 2 + len(self.header.header_rows)
+ return super().read(table)
| diff --git a/astropy/io/ascii/tests/test_rst.py b/astropy/io/ascii/tests/test_rst.py
--- a/astropy/io/ascii/tests/test_rst.py
+++ b/astropy/io/ascii/tests/test_rst.py
@@ -2,7 +2,11 @@
from io import StringIO
+import numpy as np
+
+import astropy.units as u
from astropy.io import ascii
+from astropy.table import QTable
from .common import assert_almost_equal, assert_equal
@@ -185,3 +189,27 @@ def test_write_normal():
==== ========= ==== ====
""",
)
+
+
+def test_rst_with_header_rows():
+ """Round-trip a table with header_rows specified"""
+ lines = [
+ "======= ======== ====",
+ " wave response ints",
+ " nm ct ",
+ "float64 float32 int8",
+ "======= ======== ====",
+ " 350.0 1.0 1",
+ " 950.0 2.0 2",
+ "======= ======== ====",
+ ]
+ tbl = QTable.read(lines, format="ascii.rst", header_rows=["name", "unit", "dtype"])
+ assert tbl["wave"].unit == u.nm
+ assert tbl["response"].unit == u.ct
+ assert tbl["wave"].dtype == np.float64
+ assert tbl["response"].dtype == np.float32
+ assert tbl["ints"].dtype == np.int8
+
+ out = StringIO()
+ tbl.write(out, format="ascii.rst", header_rows=["name", "unit", "dtype"])
+ assert out.getvalue().splitlines() == lines
| Please support header rows in RestructuredText output
### Description
It would be great if the following would work:
```Python
>>> from astropy.table import QTable
>>> import astropy.units as u
>>> import sys
>>> tbl = QTable({'wave': [350,950]*u.nm, 'response': [0.7, 1.2]*u.count})
>>> tbl.write(sys.stdout, format="ascii.rst")
===== ========
wave response
===== ========
350.0 0.7
950.0 1.2
===== ========
>>> tbl.write(sys.stdout, format="ascii.fixed_width", header_rows=["name", "unit"])
| wave | response |
| nm | ct |
| 350.0 | 0.7 |
| 950.0 | 1.2 |
>>> tbl.write(sys.stdout, format="ascii.rst", header_rows=["name", "unit"])
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3/dist-packages/astropy/table/connect.py", line 129, in __call__
self.registry.write(instance, *args, **kwargs)
File "/usr/lib/python3/dist-packages/astropy/io/registry/core.py", line 369, in write
return writer(data, *args, **kwargs)
File "/usr/lib/python3/dist-packages/astropy/io/ascii/connect.py", line 26, in io_write
return write(table, filename, **kwargs)
File "/usr/lib/python3/dist-packages/astropy/io/ascii/ui.py", line 856, in write
writer = get_writer(Writer=Writer, fast_writer=fast_writer, **kwargs)
File "/usr/lib/python3/dist-packages/astropy/io/ascii/ui.py", line 800, in get_writer
writer = core._get_writer(Writer, fast_writer, **kwargs)
File "/usr/lib/python3/dist-packages/astropy/io/ascii/core.py", line 1719, in _get_writer
writer = Writer(**writer_kwargs)
TypeError: RST.__init__() got an unexpected keyword argument 'header_rows'
```
### Additional context
RestructuredText output is a great way to fill autogenerated documentation with content, so having this flexible makes the life easier `:-)`
| 2022-12-16T11:13:37Z | 5.1 | ["astropy/io/ascii/tests/test_rst.py::test_rst_with_header_rows"] | ["astropy/io/ascii/tests/test_rst.py::test_read_normal", "astropy/io/ascii/tests/test_rst.py::test_read_normal_names", "astropy/io/ascii/tests/test_rst.py::test_read_normal_names_include", "astropy/io/ascii/tests/test_rst.py::test_read_normal_exclude", "astropy/io/ascii/tests/test_rst.py::test_read_unbounded_right_column", "astropy/io/ascii/tests/test_rst.py::test_read_unbounded_right_column_header", "astropy/io/ascii/tests/test_rst.py::test_read_right_indented_table", "astropy/io/ascii/tests/test_rst.py::test_trailing_spaces_in_row_definition", "astropy/io/ascii/tests/test_rst.py::test_write_normal"] | 5f74eacbcc7fff707a44d8eb58adaa514cb7dcb5 |
|
astropy/astropy | astropy__astropy-14365 | 7269fa3e33e8d02485a647da91a5a2a60a06af61 | diff --git a/astropy/io/ascii/qdp.py b/astropy/io/ascii/qdp.py
--- a/astropy/io/ascii/qdp.py
+++ b/astropy/io/ascii/qdp.py
@@ -68,7 +68,7 @@ def _line_type(line, delimiter=None):
_new_re = rf"NO({sep}NO)+"
_data_re = rf"({_decimal_re}|NO|[-+]?nan)({sep}({_decimal_re}|NO|[-+]?nan))*)"
_type_re = rf"^\s*((?P<command>{_command_re})|(?P<new>{_new_re})|(?P<data>{_data_re})?\s*(\!(?P<comment>.*))?\s*$"
- _line_type_re = re.compile(_type_re)
+ _line_type_re = re.compile(_type_re, re.IGNORECASE)
line = line.strip()
if not line:
return "comment"
@@ -306,7 +306,7 @@ def _get_tables_from_qdp_file(qdp_file, input_colnames=None, delimiter=None):
values = []
for v in line.split(delimiter):
- if v == "NO":
+ if v.upper() == "NO":
values.append(np.ma.masked)
else:
# Understand if number is int or float
| diff --git a/astropy/io/ascii/tests/test_qdp.py b/astropy/io/ascii/tests/test_qdp.py
--- a/astropy/io/ascii/tests/test_qdp.py
+++ b/astropy/io/ascii/tests/test_qdp.py
@@ -43,7 +43,18 @@ def test_get_tables_from_qdp_file(tmp_path):
assert np.isclose(table2["MJD_nerr"][0], -2.37847222222222e-05)
-def test_roundtrip(tmp_path):
+def lowercase_header(value):
+ """Make every non-comment line lower case."""
+ lines = []
+ for line in value.splitlines():
+ if not line.startswith("!"):
+ line = line.lower()
+ lines.append(line)
+ return "\n".join(lines)
+
+
[email protected]("lowercase", [False, True])
+def test_roundtrip(tmp_path, lowercase):
example_qdp = """
! Swift/XRT hardness ratio of trigger: XXXX, name: BUBU X-2
! Columns are as labelled
@@ -70,6 +81,8 @@ def test_roundtrip(tmp_path):
53000.123456 2.37847222222222e-05 -2.37847222222222e-05 -0.292553 -0.374935
NO 1.14467592592593e-05 -1.14467592592593e-05 0.000000 NO
"""
+ if lowercase:
+ example_qdp = lowercase_header(example_qdp)
path = str(tmp_path / "test.qdp")
path2 = str(tmp_path / "test2.qdp")
| ascii.qdp Table format assumes QDP commands are upper case
### Description
ascii.qdp assumes that commands in a QDP file are upper case, for example, for errors they must be "READ SERR 1 2" whereas QDP itself is not case sensitive and case use "read serr 1 2".
As many QDP files are created by hand, the expectation that all commands be all-caps should be removed.
### Expected behavior
The following qdp file should read into a `Table` with errors, rather than crashing.
```
read serr 1 2
1 0.5 1 0.5
```
### How to Reproduce
Create a QDP file:
```
> cat > test.qdp
read serr 1 2
1 0.5 1 0.5
<EOF>
> python
Python 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from astropy.table import Table
>>> Table.read('test.qdp',format='ascii.qdp')
WARNING: table_id not specified. Reading the first available table [astropy.io.ascii.qdp]
Traceback (most recent call last):
...
raise ValueError(f'Unrecognized QDP line: {line}')
ValueError: Unrecognized QDP line: read serr 1 2
```
Running "qdp test.qdp" works just fine.
### Versions
Python 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)]
astropy 5.1
Numpy 1.24.1
pyerfa 2.0.0.1
Scipy 1.10.0
Matplotlib 3.6.3
| Welcome to Astropy 👋 and thank you for your first issue!
A project member will respond to you as soon as possible; in the meantime, please double-check the [guidelines for submitting issues](https://github.com/astropy/astropy/blob/main/CONTRIBUTING.md#reporting-issues) and make sure you've provided the requested details.
GitHub issues in the Astropy repository are used to track bug reports and feature requests; If your issue poses a question about how to use Astropy, please instead raise your question in the [Astropy Discourse user forum](https://community.openastronomy.org/c/astropy/8) and close this issue.
If you feel that this issue has not been responded to in a timely manner, please send a message directly to the [development mailing list](http://groups.google.com/group/astropy-dev). If the issue is urgent or sensitive in nature (e.g., a security vulnerability) please send an e-mail directly to the private e-mail [email protected].
Huh, so we do have this format... https://docs.astropy.org/en/stable/io/ascii/index.html
@taldcroft , you know anything about this?
This is the format I'm using, which has the issue: https://docs.astropy.org/en/stable/api/astropy.io.ascii.QDP.html
The issue is that the regex that searches for QDP commands is not case insensitive.
This attached patch fixes the issue, but I'm sure there's a better way of doing it.
[qdp.patch](https://github.com/astropy/astropy/files/10667923/qdp.patch)
@jak574 - the fix is probably as simple as that. Would you like to put in a bugfix PR? | 2023-02-06T19:20:34Z | 5.1 | ["astropy/io/ascii/tests/test_qdp.py::test_roundtrip[True]"] | ["astropy/io/ascii/tests/test_qdp.py::test_get_tables_from_qdp_file", "astropy/io/ascii/tests/test_qdp.py::test_roundtrip[False]", "astropy/io/ascii/tests/test_qdp.py::test_read_example", "astropy/io/ascii/tests/test_qdp.py::test_roundtrip_example", "astropy/io/ascii/tests/test_qdp.py::test_roundtrip_example_comma", "astropy/io/ascii/tests/test_qdp.py::test_read_write_simple", "astropy/io/ascii/tests/test_qdp.py::test_read_write_simple_specify_name", "astropy/io/ascii/tests/test_qdp.py::test_get_lines_from_qdp"] | 5f74eacbcc7fff707a44d8eb58adaa514cb7dcb5 |
astropy/astropy | astropy__astropy-14995 | b16c7d12ccbc7b2d20364b89fb44285bcbfede54 | diff --git a/astropy/nddata/mixins/ndarithmetic.py b/astropy/nddata/mixins/ndarithmetic.py
--- a/astropy/nddata/mixins/ndarithmetic.py
+++ b/astropy/nddata/mixins/ndarithmetic.py
@@ -520,10 +520,10 @@ def _arithmetic_mask(self, operation, operand, handle_mask, axis=None, **kwds):
elif self.mask is None and operand is not None:
# Make a copy so there is no reference in the result.
return deepcopy(operand.mask)
- elif operand is None:
+ elif operand.mask is None:
return deepcopy(self.mask)
else:
- # Now lets calculate the resulting mask (operation enforces copy)
+ # Now let's calculate the resulting mask (operation enforces copy)
return handle_mask(self.mask, operand.mask, **kwds)
def _arithmetic_wcs(self, operation, operand, compare_wcs, **kwds):
| diff --git a/astropy/nddata/mixins/tests/test_ndarithmetic.py b/astropy/nddata/mixins/tests/test_ndarithmetic.py
--- a/astropy/nddata/mixins/tests/test_ndarithmetic.py
+++ b/astropy/nddata/mixins/tests/test_ndarithmetic.py
@@ -1310,3 +1310,42 @@ def test_raise_method_not_supported():
# raise error for unsupported propagation operations:
with pytest.raises(ValueError):
ndd1.uncertainty.propagate(np.mod, ndd2, result, correlation)
+
+
+def test_nddata_bitmask_arithmetic():
+ # NDData.mask is usually assumed to be boolean, but could be
+ # a bitmask. Ensure bitmask works:
+ array = np.array([[0, 1, 0], [1, 0, 1], [0, 1, 0]])
+ mask = np.array([[0, 1, 64], [8, 0, 1], [2, 1, 0]])
+
+ nref_nomask = NDDataRef(array)
+ nref_masked = NDDataRef(array, mask=mask)
+
+ # multiply no mask by constant (no mask * no mask)
+ assert nref_nomask.multiply(1.0, handle_mask=np.bitwise_or).mask is None
+
+ # multiply no mask by itself (no mask * no mask)
+ assert nref_nomask.multiply(nref_nomask, handle_mask=np.bitwise_or).mask is None
+
+ # multiply masked by constant (mask * no mask)
+ np.testing.assert_equal(
+ nref_masked.multiply(1.0, handle_mask=np.bitwise_or).mask, mask
+ )
+
+ # multiply masked by itself (mask * mask)
+ np.testing.assert_equal(
+ nref_masked.multiply(nref_masked, handle_mask=np.bitwise_or).mask, mask
+ )
+
+ # multiply masked by no mask (mask * no mask)
+ np.testing.assert_equal(
+ nref_masked.multiply(nref_nomask, handle_mask=np.bitwise_or).mask, mask
+ )
+
+ # check bitwise logic still works
+ other_mask = np.array([[64, 1, 0], [2, 1, 0], [8, 0, 2]])
+ nref_mask_other = NDDataRef(array, mask=other_mask)
+ np.testing.assert_equal(
+ nref_mask_other.multiply(nref_masked, handle_mask=np.bitwise_or).mask,
+ np.bitwise_or(mask, other_mask),
+ )
| In v5.3, NDDataRef mask propagation fails when one of the operand does not have a mask
### Description
This applies to v5.3.
It looks like when one of the operand does not have a mask, the mask propagation when doing arithmetic, in particular with `handle_mask=np.bitwise_or` fails. This is not a problem in v5.2.
I don't know enough about how all that works, but it seems from the error that the operand without a mask is set as a mask of None's and then the bitwise_or tries to operate on an integer and a None and fails.
### Expected behavior
When one of the operand does not have mask, the mask that exists should just be copied over to the output. Or whatever was done in that situation in v5.2 where there's no problem.
### How to Reproduce
This is with v5.3. With v5.2, there are no errors.
```
>>> import numpy as np
>>> from astropy.nddata import NDDataRef
>>> array = np.array([[0, 1, 0], [1, 0, 1], [0, 1, 0]])
>>> mask = np.array([[0, 1, 64], [8, 0, 1], [2, 1, 0]])
>>> nref_nomask = NDDataRef(array)
>>> nref_mask = NDDataRef(array, mask=mask)
# multiply no mask by constant (no mask * no mask)
>>> nref_nomask.multiply(1., handle_mask=np.bitwise_or).mask # returns nothing, no mask, OK
# multiply no mask by itself (no mask * no mask)
>>> nref_nomask.multiply(nref_nomask, handle_mask=np.bitwise_or).mask # return nothing, no mask, OK
# multiply mask by constant (mask * no mask)
>>> nref_mask.multiply(1., handle_mask=np.bitwise_or).mask
...
TypeError: unsupported operand type(s) for |: 'int' and 'NoneType'
# multiply mask by itself (mask * mask)
>>> nref_mask.multiply(nref_mask, handle_mask=np.bitwise_or).mask
array([[ 0, 1, 64],
[ 8, 0, 1],
[ 2, 1, 0]])
# multiply mask by no mask (mask * no mask)
>>> nref_mask.multiply(nref_nomask, handle_mask=np.bitwise_or).mask
...
TypeError: unsupported operand type(s) for |: 'int' and 'NoneType'
```
### Versions
>>> import sys; print("Python", sys.version)
Python 3.10.11 | packaged by conda-forge | (main, May 10 2023, 19:07:22) [Clang 14.0.6 ]
>>> import astropy; print("astropy", astropy.__version__)
astropy 5.3
>>> import numpy; print("Numpy", numpy.__version__)
Numpy 1.24.3
>>> import erfa; print("pyerfa", erfa.__version__)
pyerfa 2.0.0.3
>>> import scipy; print("Scipy", scipy.__version__)
Scipy 1.10.1
>>> import matplotlib; print("Matplotlib", matplotlib.__version__)
Matplotlib 3.7.1
| Welcome to Astropy 👋 and thank you for your first issue!
A project member will respond to you as soon as possible; in the meantime, please double-check the [guidelines for submitting issues](https://github.com/astropy/astropy/blob/main/CONTRIBUTING.md#reporting-issues) and make sure you've provided the requested details.
GitHub issues in the Astropy repository are used to track bug reports and feature requests; If your issue poses a question about how to use Astropy, please instead raise your question in the [Astropy Discourse user forum](https://community.openastronomy.org/c/astropy/8) and close this issue.
If you feel that this issue has not been responded to in a timely manner, please send a message directly to the [development mailing list](http://groups.google.com/group/astropy-dev). If the issue is urgent or sensitive in nature (e.g., a security vulnerability) please send an e-mail directly to the private e-mail [email protected].
@bmorris3 , do you think this is related to that nddata feature you added in v5.3?
Hi @KathleenLabrie. I'm not sure this is a bug, because as far as I can tell the `mask` in NDData is assumed to be boolean:
https://github.com/astropy/astropy/blob/83f6f002fb11853eacb689781d366be6aa170e0e/astropy/nddata/nddata.py#L51-L55
There are updates to the propagation logic in v5.3 that allow for more flexible and customizable mask propagation, see discussion in https://github.com/astropy/astropy/pull/14175.
You're using the `bitwise_or` operation, which is different from the default `logical_or` operation in important ways. I tested your example using `logical_or` and it worked as expected, with the caveat that your mask becomes booleans with `True` for non-zero initial mask values.
We are doing data reduction. The nature of the "badness" of each pixel matters. True or False does not cut it. That why we need bits. This is scientifically required. A saturated pixel is different from a non-linear pixel, different from an unilliminated pixels, different .... etc.
I don't see why a feature that had been there for a long time was removed without even a deprecation warning.
BTW, I still think that something is broken, eg.
```
>>> bmask = np.array([[True, False, False], [False, True, False], [False, False, True]])
>>> nref_bmask = NDDataRef(array, mask=bmask)
>>> nref_bmask.multiply(1.).mask
array([[True, None, None],
[None, True, None],
[None, None, True]], dtype=object)
```
Those `None`s should probably be `False`s not None's
There is *absolutely* a bug here. Here's a demonstration:
```
>>> data = np.arange(4).reshape(2,2)
>>> mask = np.array([[1, 0], [0, 1]]))
>>> nd1 = NDDataRef(data, mask=mask)
>>> nd2 = NDDataRef(data, mask=None)
>>> nd1.multiply(nd2, handle_mask=np.bitwise_or)
...Exception...
>>> nd2.multiply(nd1, handle_mask=np.bitwise_or)
NDDataRef([[0, 1],
[4, 9]])
```
Multiplication is commutative and should still be here. In 5.2 the logic for arithmetic between two objects was that if one didn't have a `mask` or the `mask` was `None` then the output mask would be the `mask` of the other. That seems entirely sensible and I see no sensible argument for changing that. But in 5.3 the logic is that if the first operand has no mask then the output will be the mask of the second, but if the second operand has no mask then it sends both masks to the `handle_mask` function (instead of simply setting the output to the mask of the first as before).
Note that this has an unwanted effect *even if the masks are boolean*:
```
>>> bool_mask = mask.astype(bool)
>>> nd1 = NDDataRef(data, mask=bool_mask)
>>> nd2.multiply(nd1).mask
array([[False, True],
[ True, False]])
>>> nd1.multiply(nd2).mask
array([[None, True],
[True, None]], dtype=object)
```
and, whoops, the `mask` isn't a nice happy numpy `bool` array anymore.
So it looks like somebody accidentally turned the lines
```
elif operand.mask is None:
return deepcopy(self.mask)
```
into
```
elif operand is None:
return deepcopy(self.mask)
```
@chris-simpson I agree that line you suggested above is the culprit, which was [changed here](https://github.com/astropy/astropy/commit/feeb716b7412c477c694648ee1e93be2c4a73700#diff-5057de973eaa1e5036a0bef89e618b1b03fd45a9c2952655abb656822f4ddc2aL458-R498). I've reverted that specific line in a local astropy branch and verified that the existing tests still pass, and the bitmask example from @KathleenLabrie works after that line is swapped. I'll make a PR to fix this today, with a new test to make sure that we don't break this again going forward.
Many thanks for working on this, @bmorris3.
Regarding whether the `mask` is assumed to be Boolean, I had noticed in the past that some developers understood this to be the case, while others disagreed. When we discussed this back in 2016, however (as per the document you linked to in Slack), @eteq explained that the mask is just expected to be "truthy" in a NumPy sense of zero = False (unmasked) and non-zero = True (masked), which you'll see is consistent with the doc string you cited above, even if it's not entirely clear :slightly_frowning_face:.
Of course I think that flexibility is great, but I think intentional ambiguity in docs is risky when only one of the two cases is tested. 😬
Indeed, I should probably have checked that there was a test for this upstream, since I was aware of some confusion; if only we could find more time to work on these important common bits that we depend on... | 2023-06-27T19:48:18Z | 5.2 | ["astropy/nddata/mixins/tests/test_ndarithmetic.py::test_nddata_bitmask_arithmetic"] | ["astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_data[data10-data20]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_data[data11-data21]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_data[data12-data22]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_data[data13-data23]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_data[data14-data24]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_data[data15-data25]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_data[data16-data26]", 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"astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_varianceuncertainty_with_units[uncert16-uncert26]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_varianceuncertainty_with_units[uncert17-uncert27]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_varianceuncertainty_with_units[uncert18-uncert28]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_varianceuncertainty_with_units[uncert19-uncert29]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_varianceuncertainty_with_units[uncert110-uncert210]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_varianceuncertainty_with_units[uncert111-uncert211]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert10-None]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert11-None]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[None-uncert22]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[None-uncert23]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert14-uncert24]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert15-uncert25]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert16-uncert26]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert17-uncert27]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert18-uncert28]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert19-uncert29]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert110-uncert210]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_inversevarianceuncertainty_with_units[uncert111-uncert211]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_handle_switches[ff]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_handle_switches[first_found]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_meta_func", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_wcs_func", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_mask_func", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_two_argument_useage[add]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_two_argument_useage[subtract]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_two_argument_useage[divide]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_two_argument_useage[multiply]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_two_argument_useage_non_nddata_first_arg[add]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_two_argument_useage_non_nddata_first_arg[subtract]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_two_argument_useage_non_nddata_first_arg[divide]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_two_argument_useage_non_nddata_first_arg[multiply]", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_arithmetics_unknown_uncertainties", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_psf_warning", "astropy/nddata/mixins/tests/test_ndarithmetic.py::test_raise_method_not_supported"] | 362f6df12abf9bd769d4915fabf955c993ea22cf |
astropy/astropy | astropy__astropy-6938 | c76af9ed6bb89bfba45b9f5bc1e635188278e2fa | diff --git a/astropy/io/fits/fitsrec.py b/astropy/io/fits/fitsrec.py
--- a/astropy/io/fits/fitsrec.py
+++ b/astropy/io/fits/fitsrec.py
@@ -1261,7 +1261,7 @@ def _scale_back_ascii(self, col_idx, input_field, output_field):
# Replace exponent separator in floating point numbers
if 'D' in format:
- output_field.replace(encode_ascii('E'), encode_ascii('D'))
+ output_field[:] = output_field.replace(b'E', b'D')
def _get_recarray_field(array, key):
| diff --git a/astropy/io/fits/tests/test_checksum.py b/astropy/io/fits/tests/test_checksum.py
--- a/astropy/io/fits/tests/test_checksum.py
+++ b/astropy/io/fits/tests/test_checksum.py
@@ -205,9 +205,9 @@ def test_ascii_table_data(self):
# The checksum ends up being different on Windows, possibly due
# to slight floating point differences
assert 'CHECKSUM' in hdul[1].header
- assert hdul[1].header['CHECKSUM'] == '51IDA1G981GCA1G9'
+ assert hdul[1].header['CHECKSUM'] == '3rKFAoI94oICAoI9'
assert 'DATASUM' in hdul[1].header
- assert hdul[1].header['DATASUM'] == '1948208413'
+ assert hdul[1].header['DATASUM'] == '1914653725'
def test_compressed_image_data(self):
with fits.open(self.data('comp.fits')) as h1:
diff --git a/astropy/io/fits/tests/test_table.py b/astropy/io/fits/tests/test_table.py
--- a/astropy/io/fits/tests/test_table.py
+++ b/astropy/io/fits/tests/test_table.py
@@ -298,6 +298,19 @@ def test_ascii_table(self):
hdul = fits.open(self.temp('toto.fits'))
assert comparerecords(hdu.data, hdul[1].data)
hdul.close()
+
+ # Test Scaling
+
+ r1 = np.array([11., 12.])
+ c2 = fits.Column(name='def', format='D', array=r1, bscale=2.3,
+ bzero=0.6)
+ hdu = fits.TableHDU.from_columns([c2])
+ hdu.writeto(self.temp('toto.fits'), overwrite=True)
+ with open(self.temp('toto.fits')) as f:
+ assert '4.95652173913043548D+00' in f.read()
+ with fits.open(self.temp('toto.fits')) as hdul:
+ assert comparerecords(hdu.data, hdul[1].data)
+
a.close()
def test_endianness(self):
| Possible bug in io.fits related to D exponents
I came across the following code in ``fitsrec.py``:
```python
# Replace exponent separator in floating point numbers
if 'D' in format:
output_field.replace(encode_ascii('E'), encode_ascii('D'))
```
I think this may be incorrect because as far as I can tell ``replace`` is not an in-place operation for ``chararray`` (it returns a copy). Commenting out this code doesn't cause any tests to fail so I think this code isn't being tested anyway.
| It is tested with `astropy/io/fits/tests/test_checksum.py:test_ascii_table_data` but indeed the operation is not inplace and it does not fail. Using 'D' is probably better, but since #5362 (I had vague memory about something like this ^^, see also #5353) anyway 'D' and 'E' are read as double, so I think there is not difference on Astropy side. | 2017-12-07T00:01:14Z | 1.3 | ["astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_ascii_table_data", "astropy/io/fits/tests/test_table.py::TestTableFunctions::test_ascii_table"] | ["astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_sample_file", "astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_image_create", "astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_scaled_data", "astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_scaled_data_auto_rescale", "astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_uint16_data", "astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_groups_hdu_data", "astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_open_with_no_keywords", "astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_writeto_convenience", "astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_hdu_writeto", "astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_datasum_only", "astropy/io/fits/tests/test_table.py::test_regression_scalar_indexing"] | 848c8fa21332abd66b44efe3cb48b72377fb32cc |
astropy/astropy | astropy__astropy-7746 | d5bd3f68bb6d5ce3a61bdce9883ee750d1afade5 | diff --git a/astropy/wcs/wcs.py b/astropy/wcs/wcs.py
--- a/astropy/wcs/wcs.py
+++ b/astropy/wcs/wcs.py
@@ -1212,6 +1212,9 @@ def _array_converter(self, func, sky, *args, ra_dec_order=False):
"""
def _return_list_of_arrays(axes, origin):
+ if any([x.size == 0 for x in axes]):
+ return axes
+
try:
axes = np.broadcast_arrays(*axes)
except ValueError:
@@ -1235,6 +1238,8 @@ def _return_single_array(xy, origin):
raise ValueError(
"When providing two arguments, the array must be "
"of shape (N, {0})".format(self.naxis))
+ if 0 in xy.shape:
+ return xy
if ra_dec_order and sky == 'input':
xy = self._denormalize_sky(xy)
result = func(xy, origin)
| diff --git a/astropy/wcs/tests/test_wcs.py b/astropy/wcs/tests/test_wcs.py
--- a/astropy/wcs/tests/test_wcs.py
+++ b/astropy/wcs/tests/test_wcs.py
@@ -1093,3 +1093,21 @@ def test_keyedsip():
assert isinstance( w.sip, wcs.Sip )
assert w.sip.crpix[0] == 2048
assert w.sip.crpix[1] == 1026
+
+
+def test_zero_size_input():
+ with fits.open(get_pkg_data_filename('data/sip.fits')) as f:
+ w = wcs.WCS(f[0].header)
+
+ inp = np.zeros((0, 2))
+ assert_array_equal(inp, w.all_pix2world(inp, 0))
+ assert_array_equal(inp, w.all_world2pix(inp, 0))
+
+ inp = [], [1]
+ result = w.all_pix2world([], [1], 0)
+ assert_array_equal(inp[0], result[0])
+ assert_array_equal(inp[1], result[1])
+
+ result = w.all_world2pix([], [1], 0)
+ assert_array_equal(inp[0], result[0])
+ assert_array_equal(inp[1], result[1])
| Issue when passing empty lists/arrays to WCS transformations
The following should not fail but instead should return empty lists/arrays:
```
In [1]: from astropy.wcs import WCS
In [2]: wcs = WCS('2MASS_h.fits')
In [3]: wcs.wcs_pix2world([], [], 0)
---------------------------------------------------------------------------
InconsistentAxisTypesError Traceback (most recent call last)
<ipython-input-3-e2cc0e97941a> in <module>()
----> 1 wcs.wcs_pix2world([], [], 0)
~/Dropbox/Code/Astropy/astropy/astropy/wcs/wcs.py in wcs_pix2world(self, *args, **kwargs)
1352 return self._array_converter(
1353 lambda xy, o: self.wcs.p2s(xy, o)['world'],
-> 1354 'output', *args, **kwargs)
1355 wcs_pix2world.__doc__ = """
1356 Transforms pixel coordinates to world coordinates by doing
~/Dropbox/Code/Astropy/astropy/astropy/wcs/wcs.py in _array_converter(self, func, sky, ra_dec_order, *args)
1267 "a 1-D array for each axis, followed by an origin.")
1268
-> 1269 return _return_list_of_arrays(axes, origin)
1270
1271 raise TypeError(
~/Dropbox/Code/Astropy/astropy/astropy/wcs/wcs.py in _return_list_of_arrays(axes, origin)
1223 if ra_dec_order and sky == 'input':
1224 xy = self._denormalize_sky(xy)
-> 1225 output = func(xy, origin)
1226 if ra_dec_order and sky == 'output':
1227 output = self._normalize_sky(output)
~/Dropbox/Code/Astropy/astropy/astropy/wcs/wcs.py in <lambda>(xy, o)
1351 raise ValueError("No basic WCS settings were created.")
1352 return self._array_converter(
-> 1353 lambda xy, o: self.wcs.p2s(xy, o)['world'],
1354 'output', *args, **kwargs)
1355 wcs_pix2world.__doc__ = """
InconsistentAxisTypesError: ERROR 4 in wcsp2s() at line 2646 of file cextern/wcslib/C/wcs.c:
ncoord and/or nelem inconsistent with the wcsprm.
```
| 2018-08-20T14:07:20Z | 1.3 | ["astropy/wcs/tests/test_wcs.py::test_zero_size_input"] | ["astropy/wcs/tests/test_wcs.py::TestMaps::test_consistency", "astropy/wcs/tests/test_wcs.py::TestMaps::test_maps", "astropy/wcs/tests/test_wcs.py::TestSpectra::test_consistency", "astropy/wcs/tests/test_wcs.py::TestSpectra::test_spectra", "astropy/wcs/tests/test_wcs.py::test_fixes", "astropy/wcs/tests/test_wcs.py::test_outside_sky", "astropy/wcs/tests/test_wcs.py::test_pix2world", "astropy/wcs/tests/test_wcs.py::test_load_fits_path", "astropy/wcs/tests/test_wcs.py::test_dict_init", "astropy/wcs/tests/test_wcs.py::test_extra_kwarg", "astropy/wcs/tests/test_wcs.py::test_3d_shapes", "astropy/wcs/tests/test_wcs.py::test_preserve_shape", "astropy/wcs/tests/test_wcs.py::test_broadcasting", "astropy/wcs/tests/test_wcs.py::test_shape_mismatch", "astropy/wcs/tests/test_wcs.py::test_invalid_shape", "astropy/wcs/tests/test_wcs.py::test_warning_about_defunct_keywords", "astropy/wcs/tests/test_wcs.py::test_warning_about_defunct_keywords_exception", "astropy/wcs/tests/test_wcs.py::test_to_header_string", "astropy/wcs/tests/test_wcs.py::test_to_fits", "astropy/wcs/tests/test_wcs.py::test_to_header_warning", "astropy/wcs/tests/test_wcs.py::test_no_comments_in_header", "astropy/wcs/tests/test_wcs.py::test_find_all_wcs_crash", "astropy/wcs/tests/test_wcs.py::test_validate", "astropy/wcs/tests/test_wcs.py::test_validate_with_2_wcses", "astropy/wcs/tests/test_wcs.py::test_crpix_maps_to_crval", "astropy/wcs/tests/test_wcs.py::test_all_world2pix", "astropy/wcs/tests/test_wcs.py::test_scamp_sip_distortion_parameters", "astropy/wcs/tests/test_wcs.py::test_fixes2", "astropy/wcs/tests/test_wcs.py::test_unit_normalization", "astropy/wcs/tests/test_wcs.py::test_footprint_to_file", "astropy/wcs/tests/test_wcs.py::test_validate_faulty_wcs", "astropy/wcs/tests/test_wcs.py::test_error_message", "astropy/wcs/tests/test_wcs.py::test_out_of_bounds", "astropy/wcs/tests/test_wcs.py::test_calc_footprint_1", "astropy/wcs/tests/test_wcs.py::test_calc_footprint_2", "astropy/wcs/tests/test_wcs.py::test_calc_footprint_3", "astropy/wcs/tests/test_wcs.py::test_sip", "astropy/wcs/tests/test_wcs.py::test_printwcs", "astropy/wcs/tests/test_wcs.py::test_invalid_spherical", "astropy/wcs/tests/test_wcs.py::test_no_iteration", "astropy/wcs/tests/test_wcs.py::test_sip_tpv_agreement", "astropy/wcs/tests/test_wcs.py::test_tpv_copy", "astropy/wcs/tests/test_wcs.py::test_hst_wcs", "astropy/wcs/tests/test_wcs.py::test_list_naxis", "astropy/wcs/tests/test_wcs.py::test_sip_broken", "astropy/wcs/tests/test_wcs.py::test_no_truncate_crval", "astropy/wcs/tests/test_wcs.py::test_no_truncate_crval_try2", "astropy/wcs/tests/test_wcs.py::test_no_truncate_crval_p17", "astropy/wcs/tests/test_wcs.py::test_no_truncate_using_compare", "astropy/wcs/tests/test_wcs.py::test_passing_ImageHDU", "astropy/wcs/tests/test_wcs.py::test_inconsistent_sip", "astropy/wcs/tests/test_wcs.py::test_bounds_check", "astropy/wcs/tests/test_wcs.py::test_naxis", "astropy/wcs/tests/test_wcs.py::test_sip_with_altkey", "astropy/wcs/tests/test_wcs.py::test_to_fits_1", "astropy/wcs/tests/test_wcs.py::test_keyedsip"] | 848c8fa21332abd66b44efe3cb48b72377fb32cc |
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