diff --git a/.flake8 b/.flake8 new file mode 100644 index 000000000..857fd4a26 --- /dev/null +++ b/.flake8 @@ -0,0 +1,5 @@ +[flake8] +max-line-length=100 +max-complexity=18 +ignore=E203, W503 +exclude=btk/__init__.py,docs/build/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 91fa32f41..55d1da21e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,7 +1,7 @@ --- repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.2.0 + rev: v4.3.0 hooks: - id: trailing-whitespace exclude: ^.*fits @@ -14,26 +14,21 @@ repos: - id: end-of-file-fixer exclude: ^.*fits - repo: https://github.com/psf/black - rev: 22.3.0 + rev: 22.6.0 hooks: - id: black language_version: python3 args: - "--line-length=100" - - repo: https://github.com/asottile/reorder_python_imports - rev: v3.1.0 + - repo: https://github.com/pycqa/isort + rev: 5.10.1 hooks: - - id: reorder-python-imports + - id: isort + name: isort (python) - repo: https://github.com/pycqa/flake8 rev: 4.0.1 hooks: - id: flake8 - args: # arguments to configure flake8 - # making isort line length compatible with black - - "--max-line-length=100" - - "--max-complexity=18" - - "--ignore=E203, W503" - - "--exclude=btk/__init__.py" - repo: https://github.com/pycqa/pydocstyle rev: 6.1.1 # pick a git hash / tag to point to hooks: diff --git a/btk/__init__.py b/btk/__init__.py index 01c674892..20c5caa17 100644 --- a/btk/__init__.py +++ b/btk/__init__.py @@ -4,21 +4,21 @@ providing a framework to test user defined detection/deblending/measurement algorithms. """ -import importlib.metadata - __author__ = "btk developers" __email__ = "imendoza@umich.edu" __version__ = "1.0.0a1" DEFAULT_SEED = 0 -from . import catalog -from . import create_blend_generator -from . import draw_blends -from . import measure -from . import metrics -from . import multiprocess -from . import plot_utils -from . import sampling_functions -from . import survey -from . import utils +from . import ( + catalog, + create_blend_generator, + draw_blends, + measure, + metrics, + multiprocess, + plot_utils, + sampling_functions, + survey, + utils, +) diff --git a/btk/catalog.py b/btk/catalog.py index fb2fa523b..237fb1500 100644 --- a/btk/catalog.py +++ b/btk/catalog.py @@ -1,7 +1,6 @@ """Contains abstract base class `Catalog` that standarizes catalog usage across BTK.""" import os -from abc import ABC -from abc import abstractmethod +from abc import ABC, abstractmethod from copy import deepcopy import astropy.table diff --git a/btk/draw_blends.py b/btk/draw_blends.py index 5da0cb0fd..80e280f90 100644 --- a/btk/draw_blends.py +++ b/btk/draw_blends.py @@ -1,24 +1,20 @@ """Module for generating batches of drawn blended images.""" import copy import os -from abc import ABC -from abc import abstractmethod +from abc import ABC, abstractmethod from collections.abc import Iterable from itertools import chain import galsim import numpy as np from astropy.table import Column -from galcheat.utilities import mag2counts -from galcheat.utilities import mean_sky_level +from galcheat.utilities import mag2counts, mean_sky_level from tqdm.auto import tqdm from btk import DEFAULT_SEED from btk.create_blend_generator import BlendGenerator -from btk.multiprocess import get_current_process -from btk.multiprocess import multiprocess -from btk.survey import make_wcs -from btk.survey import Survey +from btk.multiprocess import get_current_process, multiprocess +from btk.survey import Survey, make_wcs MAX_SEED_INT = 1_000_000_000 diff --git a/btk/multiprocess.py b/btk/multiprocess.py index 27f3ad845..496b7d594 100644 --- a/btk/multiprocess.py +++ b/btk/multiprocess.py @@ -1,7 +1,6 @@ """Tools for multiprocessing in BTK.""" import multiprocessing as mp -from itertools import repeat -from itertools import starmap +from itertools import repeat, starmap def _apply_args_and_kwargs(fn, args, kwargs): diff --git a/btk/plot_utils.py b/btk/plot_utils.py index 133f55a07..3c2136bce 100644 --- a/btk/plot_utils.py +++ b/btk/plot_utils.py @@ -7,8 +7,7 @@ import numpy as np import pandas as pd import seaborn as sns -from IPython.display import clear_output -from IPython.display import display +from IPython.display import clear_output, display def get_rgb(image, min_val=None, max_val=None): diff --git a/btk/sampling_functions.py b/btk/sampling_functions.py index 93e25f2d2..31a8e2227 100644 --- a/btk/sampling_functions.py +++ b/btk/sampling_functions.py @@ -1,13 +1,11 @@ """Contains classes of function for extracing information from catalog in blend batches.""" import warnings -from abc import ABC -from abc import abstractmethod +from abc import ABC, abstractmethod import astropy.table import numpy as np from btk import DEFAULT_SEED -from btk.catalog import CatsimCatalog def _get_random_center_shift(num_objects, maxshift, rng): @@ -193,185 +191,3 @@ def __call__(self, table, **kwargs): blend_table["ra"] += x_peak blend_table["dec"] += y_peak return blend_table - - -class GroupSampling(SamplingFunction): - """Uses a pre-analyzed WLD catalog to draw blends.""" - - def __init__( - self, - max_number, - wld_catalog_name, - stamp_size, - pixel_scale, - shift=None, - group_id=None, - seed=DEFAULT_SEED, - ): - """Blends are defined from *groups* of galaxies from a CatSim-like catalog. - - Note: the pre-run WLD images are not used here. We only use the pre-run - catalog (in i band) to identify galaxies that belong to a group. - - Args: - max_number (int): Same as in SamplingFunction - wld_catalog_name: File path to a pre-analyzed WLD Catsim catalog - stamp_size (int): Size of the generated stamps - pixel_scale (float): pixel scale of the survey, in arcseconds per pixel - shift (list): List containing shifts to apply (useful to avoid randomization) - group_id (list): List containing which group_ids to analyze (avoid randomization) - seed (int): Seed to initialize randomness for reproducibility. - """ - super().__init__(max_number, seed) - - self.wld_catalog = CatsimCatalog.from_file(wld_catalog_name).get_raw_catalog() - self.stamp_size = stamp_size - self.pixel_scale = pixel_scale - self.shift = shift - self.group_id = group_id - - @property - def compatible_catalogs(self): - """Tuple of compatible catalogs for this sampling function.""" - return ("CatsimCatalog",) - - def __call__(self, table, **kwargs): - """Retrun blend info based on self.wld_catalog. - - We use self.wld_catalog created above to sample groups, but ultimately returns - rows from the input ``table`` (by matching the corresponding galaxy ids). The group is - centered on the middle of the postage stamp. Function only draws galaxies that lie within - the postage stamp size. - """ - # randomly sample a group om wld_catalog - bool_groups = self.wld_catalog["grp_size"] >= 2 - group_ids = np.unique(self.wld_catalog["grp_id"][bool_groups]) - if self.group_id is None: - group_id = self.rng.choice(group_ids, replace=False) - else: - group_id = self.group_id - - # get all galaxies belonging to the group. - ids = self.wld_catalog["db_id"][self.wld_catalog["grp_id"] == group_id] - blend_table = astropy.table.vstack([table[table["galtileid"] == i] for i in ids]) - - # Set mean x and y coordinates of the group galaxies to the center of the - # postage stamp. - blend_table["ra"] -= np.mean(blend_table["ra"]) - blend_table["dec"] -= np.mean(blend_table["dec"]) - - # Add small random shift so that center does not perfectly align with - # the stamp center - if self.shift is None: - x_peak, y_peak = _get_random_center_shift( - 1, maxshift=3 * self.pixel_scale, rng=self.rng - ) - else: - x_peak, y_peak = self.shift - blend_table["ra"] += x_peak - blend_table["dec"] += y_peak - # make sure galaxy centers don't lie too close to edge - cond1 = np.abs(blend_table["ra"]) < self.stamp_size / 2.0 - 3 - cond2 = np.abs(blend_table["dec"]) < self.stamp_size / 2.0 - 3 - no_boundary = blend_table[cond1 & cond2] - if len(no_boundary) == 0: - return no_boundary - # make sure number of galaxies in blend is less than self.max_number - # randomly select max_number of objects if larger. - num = min([len(no_boundary), self.max_number]) - select = self.rng.choice(range(len(no_boundary)), num, replace=False) - return no_boundary[select] - - -class GroupSamplingNumbered(SamplingFunction): - """Defines blends based on previously analyzed WLD catalog & exits once all groups are used.""" - - def __init__( - self, - max_number, - wld_catalog_name, - stamp_size, - pixel_scale, - shift=None, - fmt="fits", - seed=DEFAULT_SEED, - ): - """Blends defined from *groups* of galaxies from a catalog previously analyzed with WLD. - - This function has an extra attribute group_id_count which tracks the - group id returned. Each time the generator is called, 1 gets added to the - count. If the count is larger than the number of groups input, - the generator is forced to exit. - - NOTE: the pre-run WLD images are not used here. We only use the pre-run - catalog to identify galaxies that belong to a group. - - Args: - max_number: Same as SamplingFunction - wld_catalog_name: Same as GroupSamplingFunction - stamp_size (int): Size of the generated stamps - pixel_scale (float): pixel scale of the survey, in arcseconds per pixel - fmt (str): Format of input wld_catalog used to define groups. - shift (list): List of shifts to apply (usefult to avoid randomization) - seed (int): Seed to initialize randomness for reproducibility. - """ - super().__init__(max_number, seed) - self.wld_catalog = astropy.table.Table.read(wld_catalog_name, format=fmt) - self.stamp_size = stamp_size - self.pixel_scale = pixel_scale - self.group_id_count = 0 - self.shift = shift - - @property - def compatible_catalogs(self): - """Tuple of compatible catalogs for this sampling function.""" - return ("CatsimCatalog",) - - def __call__(self, table, **kwargs): - """Return info for one blend from a given astropy table based on groups from wld_catalog. - - The group is centered on the middle of the postage stamp. This function only returns - galaxies whose centers lie within 1 arcsec the postage stamp edge, which may cause the - number of galaxies in the blend to be smaller than the group size. - """ - # randomly sample a group. - group_ids = np.unique( - self.wld_catalog["grp_id"][ - (self.wld_catalog["grp_size"] >= 2) - & (self.wld_catalog["grp_size"] <= self.max_number) - ] - ) - if self.group_id_count >= len(group_ids): - message = "group_id_count is larger than number of groups input" - raise GeneratorExit(message) - - group_id = group_ids[self.group_id_count] - self.group_id_count += 1 - # get all galaxies belonging to the group. - # make sure some group or galaxy was not repeated in wld_catalog - ids = np.unique(self.wld_catalog["db_id"][self.wld_catalog["grp_id"] == group_id]) - blend_table = astropy.table.vstack([table[table["galtileid"] == i] for i in ids]) - # Set mean x and y coordinates of the group galaxies to the center of the - # postage stamp. - blend_table["ra"] -= np.mean(blend_table["ra"]) - blend_table["dec"] -= np.mean(blend_table["dec"]) - # Add small random shift so that center does not perfectly align with stamp - # center - if self.shift is None: - x_peak, y_peak = _get_random_center_shift( - 1, maxshift=5 * self.pixel_scale, rng=self.rng - ) - else: - x_peak, y_peak = self.shift - blend_table["ra"] += x_peak - blend_table["dec"] += y_peak - # make sure galaxy centers don't lie too close to edge - cond1 = np.abs(blend_table["ra"]) < self.stamp_size / 2.0 - 1 - cond2 = np.abs(blend_table["dec"]) < self.stamp_size / 2.0 - 1 - no_boundary = blend_table[cond1 & cond2] - message = ( - "Number of galaxies greater than max number of objects per" - f"blend. Found {len(no_boundary)}, expected <= {self.max_number}" - ) - assert len(no_boundary) <= self.max_number, message - return no_boundary diff --git a/btk/survey.py b/btk/survey.py index 557c5eb8e..c96933d43 100644 --- a/btk/survey.py +++ b/btk/survey.py @@ -1,9 +1,7 @@ """Contains information for surveys available in BTK.""" import os import random as rd -from typing import Callable -from typing import List -from typing import Union +from typing import Callable, List, Union import astropy.wcs as WCS import galcheat diff --git a/data/sample_dc2_group_catalog.fits b/data/sample_dc2_group_catalog.fits deleted file mode 100644 index 60d0c64f5..000000000 --- a/data/sample_dc2_group_catalog.fits +++ /dev/null @@ -1,54 +0,0 @@ -SIMPLE = T / conforms to FITS standard BITPIX = 8 / array data type NAXIS = 0 / number of array dimensions EXTEND = T END XTENSION= 'BINTABLE' / binary table extension BITPIX = 8 / array data type NAXIS = 2 / number of array dimensions NAXIS1 = 110 / length of dimension 1 NAXIS2 = 61 / length of dimension 2 PCOUNT = 0 / number of group parameters GCOUNT = 1 / number of groups TFIELDS = 27 / number of table fields TTYPE1 = 'db_id ' TFORM1 = 'K ' TNULL1 = 999999 TTYPE2 = 'grp_id ' TFORM2 = 'K ' TNULL2 = 999999 TTYPE3 = 'grp_size' TFORM3 = 'I ' TNULL3 = 16959 TTYPE4 = 'grp_rank' TFORM4 = 'I ' TNULL4 = 16959 TTYPE5 = 'visible ' TFORM5 = 'I ' TNULL5 = 16959 TTYPE6 = 'xmin ' TFORM6 = 'J ' TNULL6 = 999999 TTYPE7 = 'xmax ' TFORM7 = 'J ' TNULL7 = 999999 TTYPE8 = 'ymin ' TFORM8 = 'J ' TNULL8 = 999999 TTYPE9 = 'ymax ' TFORM9 = 'J ' TNULL9 = 999999 TTYPE10 = 'f_disk ' TFORM10 = 'E ' TTYPE11 = 'f_bulge ' TFORM11 = 'E ' TTYPE12 = 'dx ' TFORM12 = 'E ' TTYPE13 = 'dy ' TFORM13 = 'E ' TTYPE14 = 'z ' TFORM14 = 'E ' TTYPE15 = 'ab_mag ' TFORM15 = 'E ' TTYPE16 = 'ri_color' TFORM16 = 'E ' TTYPE17 = 'flux ' TFORM17 = 'E ' TTYPE18 = 'sigma_m ' TFORM18 = 'E ' TTYPE19 = 'sigma_p ' TFORM19 = 'E ' TTYPE20 = 'e1 ' TFORM20 = 'E ' TTYPE21 = 'e2 ' TFORM21 = 'E ' TTYPE22 = 'a ' TFORM22 = 'E ' TTYPE23 = 'b ' TFORM23 = 'E ' TTYPE24 = 'beta ' TFORM24 = 'E ' TTYPE25 = 'psf_sigm' TFORM25 = 'E ' TTYPE26 = 'purity ' TFORM26 = 'E ' TTYPE27 = 'snr_sky ' TFORM27 = 'E ' END o�:�o�:��� -� -�?1a>�=�C�4�B��<���A�s�>�@K�.@`�@a�4=�g���@quy@Q9� -�@d,?wrAD���oĻ$o�:��� -� -�>�`?xPC��zB�>�1HA��q? -b E��e>�G�>��,�S�=H�_>�3�>z2?�|�?,>�^S?���o�to�:��� -� -�?�C�WUBϣa>� }A�[�>JcF��>�$�>��ý�V���5�>��->q�ÿ�DA?-�Y=��,@��Do��[o�:��� -� -�>�1�?�C�5B�S�>�[A��?P'Hx ?.Tu?.�;= ->�=C�H?8�H?$k�>�?k�>��B�U�o��\o�:��� -� -�?a�M=�M�C��&B��x>��A��>� �F�N�>�|E?�? -�S���8?Hz�>�U���?K��?]NAt#o˫o�:��� -� -�?Y�7>W$C��B�7$?h�A�$�?3n�H���?� �?�|L�(f���Π?��P?Ȏ����k?���>�'!B�m�o㡾o�:��� -� -�?Y%f>jfC�/�B�n?v��Aŵw?z~�Ff��>_yh>i��=���>L�8>��*>3Ѫ?:�?(�s?$U�A ;p�>�o�:��� -� -�>P ?K�}C��Bؖ�@c�A�*��E�X�>i�>��<6SD��ʺ>)�`> z�9�4?#j>6�?���o�:�o�:��� -?��)�míSG<��UA�9�>&�H+*??.�?�^�>���>r8z?�§>�Z�>jT8?��Z?x�RB�Ro�8�o�:�� ?d� -=���!�_ì��?`6A��?�7�GEƿ>��>�#�= �Ӿ��c?�(>�`��:9�?Hn�?S}�Aߪ�oސ�o�:���  >��?.w��'ܺì�H?c��A��;��'k]C��=Am�A���>�I�I��d?� -�?�C�4���!?���?�����H�?��?{B�C���oٝ�o�;����?a��=�q��&��C�'?Y�gA�� ?�uF!�x><ɻK�~;T0>��>�?��R?!�\=r�C@���o���o�;����?rv=X� �&�C���?��A�Â>��F6:�=rm�=�7>�!�����=��#=.C@���?1�>j��A�/p��o�;����� >J�<�#�K��>I�=��?� ?!�>Dp9A;�Do�;Yo�;Y =a�?��ê�C�te=m9A�l�>��JP�n?ْ�?�� ��:�� -BF?���?�ῂb:?��?}�D<.4oɺro�;Y&,tz?$�<>�ׇ��>zC�(6?�-A���?; `F�>$;�>$<��;w�!Nr>$��>#�P���?#��=��A�?Go�rPo�;Y58hl>�J?}[���C��Z?F\�Aɓ�?��F�!>5�>6 �<�0��7�>;r%>0�۾��3?$��? -�M@��o�=�o�;Y(+��?�t:>/A��8_C��}?S<�A��?N�F -��=��C>D4��H?>۲�>4��=j�?��e?!lj>-�c@���o�;fo�;fJ�  ^?}Y!<)��âS�B��m=G-�A�_>��KP��@ �[@-���HȄ>�U)@V�?�?_��@&�?ͶE �o���o�;fbf  ?�ãǹB�f�>l��AȒj>@��F& �=�E=�-^>���>OC�>�=�>���?!4�=� �@���o��Vo�;fU]  ?nv�=�J�ä�B���>ٵ�A��m>x�Gcj>_��>m���>ƭ>$lo>���>-�?��5?(�?��B*0ao�w�o�;f�� E J?�àl�B�DC?2�2A�0S? 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�N \ No newline at end of file diff --git a/data/sample_group_catalog.fits b/data/sample_group_catalog.fits deleted file mode 100644 index ae1d971d3..000000000 --- a/data/sample_group_catalog.fits +++ /dev/null @@ -1,23 +0,0 @@ -SIMPLE = T / conforms to FITS standard BITPIX = 8 / array data type NAXIS = 0 / number of array dimensions EXTEND = T END XTENSION= 'BINTABLE' / binary table extension BITPIX = 8 / array data type NAXIS = 2 / number of array dimensions NAXIS1 = 170 / length of dimension 1 NAXIS2 = 35 / length of dimension 2 PCOUNT = 0 / number of group parameters GCOUNT = 1 / number of groups TFIELDS = 42 / number of table fields TTYPE1 = 'db_id ' TFORM1 = 'K ' TNULL1 = 999999 TTYPE2 = 'grp_id ' TFORM2 = 'K ' TNULL2 = 999999 TTYPE3 = 'grp_size' TFORM3 = 'I ' TNULL3 = 16959 TTYPE4 = 'grp_rank' TFORM4 = 'I ' TNULL4 = 16959 TTYPE5 = 'visible ' TFORM5 = 'I ' TNULL5 = 16959 TTYPE6 = 'xmin ' TFORM6 = 'J ' TNULL6 = 999999 TTYPE7 = 'xmax ' TFORM7 = 'J ' TNULL7 = 999999 TTYPE8 = 'ymin ' TFORM8 = 'J ' TNULL8 = 999999 TTYPE9 = 'ymax ' TFORM9 = 'J ' TNULL9 = 999999 TTYPE10 = 'f_disk ' TFORM10 = 'E ' TTYPE11 = 'f_bulge ' TFORM11 = 'E ' TTYPE12 = 'dx ' TFORM12 = 'E ' TTYPE13 = 'dy ' TFORM13 = 'E ' TTYPE14 = 'z ' TFORM14 = 'E ' TTYPE15 = 'ab_mag ' TFORM15 = 'E ' TTYPE16 = 'ri_color' TFORM16 = 'E ' TTYPE17 = 'flux ' TFORM17 = 'E ' TTYPE18 = 'sigma_m ' TFORM18 = 'E ' TTYPE19 = 'sigma_p ' TFORM19 = 'E ' TTYPE20 = 'e1 ' TFORM20 = 'E ' TTYPE21 = 'e2 ' TFORM21 = 'E ' TTYPE22 = 'a ' TFORM22 = 'E ' TTYPE23 = 'b ' TFORM23 = 'E ' TTYPE24 = 'beta ' TFORM24 = 'E ' TTYPE25 = 'psf_sigm' TFORM25 = 'E ' TTYPE26 = 'purity ' TFORM26 = 'E ' TTYPE27 = 'snr_sky ' TFORM27 = 'E ' TTYPE28 = 'snr_iso ' TFORM28 = 'E ' TTYPE29 = 'snr_grp ' TFORM29 = 'E ' TTYPE30 = 'snr_isof' TFORM30 = 'E ' TTYPE31 = 'snr_grpf' TFORM31 = 'E ' TTYPE32 = 'ds ' TFORM32 = 'E ' TTYPE33 = 'dg1 ' TFORM33 = 'E ' TTYPE34 = 'dg2 ' TFORM34 = 'E ' TTYPE35 = 'ds_grp ' TFORM35 = 'E ' TTYPE36 = 'dg1_grp ' TFORM36 = 'E ' TTYPE37 = 'dg2_grp ' TFORM37 = 'E ' TTYPE38 = 'hsm_sigm' TFORM38 = 'E ' TTYPE39 = 'hsm_e1 ' TFORM39 = 'E ' TTYPE40 = 'hsm_e2 ' TFORM40 = 'E ' TTYPE41 = 'g1_fit ' TFORM41 = 'E ' TTYPE42 = 'g2_fit ' TFORM42 = 'E ' END ]À?y]����#,go?�§?ã�?gA�o7?Wx`F'�>ȩ�>ʗ�=�u�=H��>�[q>��W>�4M?;�P>�i�@#̬@#�5@#��?�{?Eo@?�#f?�?�`?ʫ�?��H?��k>��>#,=� I]����]����2Yr?�§��ã�!>ߦA�N�=w�G�d�?�ڔ?�'����=�?��F?�/??�\&?��?n��Ae�8Ae2Ae-i@� W@��m>\�=��=�'F> I =�-`=��?l�ս7�=�|�]��^�]����17[a?�¢A(ä[�>�5UA��N>|E�?'��?'�Լ&K��m/?+U�?$w㿅ł?fÑ?f��?b�?b��?b��>#1.>"nb@�h@��@�4@�00@�;=@��>�k�� ��<�]�):�]����*5R]?�¤ 'ä��?��A���=��F��'>�;�>��������8�>��>���f�??48A?~�qAX�A�A�@��@���>��>��>��>� >�.�>���>�&�t$�$��]×)�]�u�]e~�?�ý�����?��GA�̦>��F&�>���>�z==�7<�H`>��P>���>/8�?.�?L��@L�@7@4E?���?��>?�P�?�1?���?��X?׊�?řa>�zi=���=�]�u�]�u�\gw�?}�m<d�ý���Ԕc@��A��x=��G ��> �>5'$>�����>f�=�+K�c��?$�?|�A4��A4|~A4| @�$@�T�?`|?P��?b�?�.?w��?�s>�v�? 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�{��Y;�,#@b<0URS?��2���?�O�"�?�&�_��'?Ҝ� p@r��_��N@r��_��N@<9���ղ@:�s` @:F!���@:J��T@:T��)r@:`- /��#��?ה΀c�?�����A?�1 ��<�D�_���?�|���0?�H�x@uY�!I@6y��!�@5��,�@5_!?��@51ۀ�@5� +@4�(�2@]�1�n@v}� �?�x����?�B|���h<5��[�?�9N��?ң���I@mg�/?@;lؠC@;\4���@:㉀L@: ����@9̇ �@9� _���]�:�@v}�r@�?�n����R?�(� T�;�(@?��d@:k _���@:EƠ�@:����@9���.�@9" -�R]��7@v}����?�u@�@�T��<4X���x?�?����-?�K���2@v~h����@=_L@%^@=5.0.2)", "hypothesis", "pympler", "pytest (> [[package]] name = "babel" -version = "2.10.1" +version = "2.10.3" description = "Internationalization utilities" category = "dev" optional = false @@ -146,7 +138,7 @@ lxml = ["lxml"] [[package]] name = "black" -version = "22.3.0" +version = "22.6.0" description = "The uncompromising code formatter." category = "dev" optional = false @@ -157,7 +149,7 @@ click = ">=8.0.0" mypy-extensions = ">=0.4.3" pathspec = ">=0.9.0" platformdirs = ">=2" -tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} +tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""} typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""} [package.extras] @@ -168,7 +160,7 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "bleach" -version = "5.0.0" +version = "5.0.1" description = "An easy safelist-based HTML-sanitizing tool." category = "main" optional = false @@ -179,12 +171,12 @@ six = ">=1.9.0" webencodings = "*" [package.extras] -css = ["tinycss2 (>=1.1.0)"] -dev = ["pip-tools (==6.5.1)", "pytest (==7.1.1)", "flake8 (==4.0.1)", "tox (==3.24.5)", "sphinx (==4.3.2)", "twine (==4.0.0)", "wheel (==0.37.1)", "hashin (==0.17.0)", "black (==22.3.0)", "mypy (==0.942)"] +css = ["tinycss2 (>=1.1.0,<1.2)"] +dev = ["build (==0.8.0)", "flake8 (==4.0.1)", "hashin (==0.17.0)", "pip-tools (==6.6.2)", "pytest (==7.1.2)", "Sphinx (==4.3.2)", "tox (==3.25.0)", "twine (==4.0.1)", "wheel (==0.37.1)", "black (==22.3.0)", "mypy (==0.961)"] [[package]] name = "certifi" -version = "2022.5.18.1" +version = "2022.6.15" description = "Python package for providing Mozilla's CA Bundle." category = "dev" optional = false @@ -233,7 +225,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "colorama" -version = "0.4.4" +version = "0.4.5" description = "Cross-platform colored terminal text." category = "main" optional = false @@ -241,14 +233,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "coverage" -version = "6.4" +version = "6.4.1" description = "Code coverage measurement for Python" category = "dev" optional = false python-versions = ">=3.7" [package.dependencies] -tomli = {version = "*", optional = true, markers = "python_version < \"3.11\" and extra == \"toml\""} +tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""} [package.extras] toml = ["tomli"] @@ -482,7 +474,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.11.4" +version = "4.12.0" description = "Read metadata from Python packages" category = "dev" optional = false @@ -494,11 +486,11 @@ zipp = ">=0.5" [package.extras] docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] [[package]] name = "importlib-resources" -version = "5.7.1" +version = "5.8.0" description = "Read resources from Python packages" category = "main" optional = false @@ -521,7 +513,7 @@ python-versions = "*" [[package]] name = "ipykernel" -version = "6.13.0" +version = "6.15.0" description = "IPython Kernel for Jupyter" category = "main" optional = false @@ -536,11 +528,12 @@ matplotlib-inline = ">=0.1" nest-asyncio = "*" packaging = "*" psutil = "*" +pyzmq = ">=17" tornado = ">=6.1" traitlets = ">=5.1.0" [package.extras] -test = ["pytest (>=6.0)", "pytest-cov", "flaky", "ipyparallel", "pre-commit", "pytest-timeout"] +test = ["flaky", "ipyparallel", "pre-commit", "pytest-cov", "pytest-timeout", "pytest (>=6.0)"] [[package]] name = "ipython" @@ -587,7 +580,7 @@ python-versions = "*" [[package]] name = "ipywidgets" -version = "7.7.0" +version = "7.7.1" description = "IPython HTML widgets for Jupyter" category = "main" optional = false @@ -598,13 +591,26 @@ ipykernel = ">=4.5.1" ipython = {version = ">=4.0.0", markers = "python_version >= \"3.3\""} ipython-genutils = ">=0.2.0,<0.3.0" jupyterlab-widgets = {version = ">=1.0.0", markers = "python_version >= \"3.6\""} -nbformat = ">=4.2.0" traitlets = ">=4.3.1" widgetsnbextension = ">=3.6.0,<3.7.0" [package.extras] test = ["pytest (>=3.6.0)", "pytest-cov", "mock"] +[[package]] +name = "isort" +version = "5.10.1" +description = "A Python utility / library to sort Python imports." +category = "dev" +optional = false +python-versions = ">=3.6.1,<4.0" + +[package.extras] +pipfile_deprecated_finder = ["pipreqs", "requirementslib"] +requirements_deprecated_finder = ["pipreqs", "pip-api"] +colors = ["colorama (>=0.4.3,<0.5.0)"] +plugins = ["setuptools"] + [[package]] name = "jedi" version = "0.18.1" @@ -636,7 +642,7 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "jsonschema" -version = "4.5.1" +version = "4.6.0" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -649,11 +655,11 @@ pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2" [package.extras] format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] -format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] +format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] [[package]] name = "jupyter-client" -version = "7.3.1" +version = "7.3.4" description = "Jupyter protocol implementation and client libraries" category = "main" optional = false @@ -664,12 +670,12 @@ entrypoints = "*" jupyter-core = ">=4.9.2" nest-asyncio = ">=1.5.4" python-dateutil = ">=2.8.2" -pyzmq = ">=22.3" +pyzmq = ">=23.0" tornado = ">=6.0" traitlets = "*" [package.extras] -doc = ["ipykernel", "myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"] +doc = ["ipykernel", "myst-parser", "sphinx-rtd-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt"] test = ["codecov", "coverage", "ipykernel (>=6.5)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"] [[package]] @@ -689,7 +695,7 @@ test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] [[package]] name = "jupyter-sphinx" -version = "0.3.2" +version = "0.4.0" description = "Jupyter Sphinx Extensions" category = "dev" optional = false @@ -712,7 +718,7 @@ python-versions = ">=3.7" [[package]] name = "jupyterlab-widgets" -version = "1.1.0" +version = "1.1.1" description = "A JupyterLab extension." category = "main" optional = false @@ -720,7 +726,7 @@ python-versions = ">=3.6" [[package]] name = "kiwisolver" -version = "1.4.2" +version = "1.4.3" description = "A fast implementation of the Cassowary constraint solver" category = "main" optional = false @@ -906,7 +912,7 @@ python-versions = ">=3.5" [[package]] name = "networkx" -version = "2.8.2" +version = "2.8.4" description = "Python package for creating and manipulating graphs and networks" category = "main" optional = false @@ -914,22 +920,22 @@ python-versions = ">=3.8" [package.extras] default = ["numpy (>=1.19)", "scipy (>=1.8)", "matplotlib (>=3.4)", "pandas (>=1.3)"] -developer = ["pre-commit (>=2.18)", "mypy (>=0.942)"] -doc = ["sphinx (>=4.5)", "pydata-sphinx-theme (>=0.8.1)", "sphinx-gallery (>=0.10)", "numpydoc (>=1.3)", "pillow (>=9.1)", "nb2plots (>=0.6)", "texext (>=0.6.6)"] +developer = ["pre-commit (>=2.19)", "mypy (>=0.960)"] +doc = ["sphinx (>=5)", "pydata-sphinx-theme (>=0.9)", "sphinx-gallery (>=0.10)", "numpydoc (>=1.4)", "pillow (>=9.1)", "nb2plots (>=0.6)", "texext (>=0.6.6)"] extra = ["lxml (>=4.6)", "pygraphviz (>=1.9)", "pydot (>=1.4.2)", "sympy (>=1.10)"] test = ["pytest (>=7.1)", "pytest-cov (>=3.0)", "codecov (>=2.1)"] [[package]] name = "nodeenv" -version = "1.6.0" +version = "1.7.0" description = "Node.js virtual environment builder" category = "dev" optional = false -python-versions = "*" +python-versions = 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"sha256:c4f6e5bbf48e74f7a38e7cc5b0480ff42b0ae5178957d564d18932525d5cf099"}, diff --git a/pyproject.toml b/pyproject.toml index 34a13f511..445fdba61 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,6 +45,7 @@ tqdm = ">=4.64.0" black = ">=22.3.0" flake8 = ">=4.0.1" flake8-absolute-import = ">=1.0" +isort = ">=5.10.1" jupyter-sphinx = ">=0.3.2" nbstripout = ">=0.5.0" nbval = ">=0.9.6" @@ -52,7 +53,6 @@ pre-commit = ">=2.18.1" pydocstyle = ">=5.1.1" pytest = ">=7.1.1" pytest-cov = ">=3.0.0" -reorder-python-imports = ">=2.6.0" sphinx = ">=3.5.4" sphinx-rtd-theme = ">=0.4.3" @@ -63,6 +63,9 @@ sphinx-rtd-theme = ">=0.4.3" line-length = 100 target-version = ['py38', 'py39'] +[tool.isort] +profile = "black" + [tool.pytest.ini_options] addopts = "-ra" filterwarnings = [ diff --git a/tests/test_catalog.py b/tests/test_catalog.py index f3d50cda6..65e6c1f25 100644 --- a/tests/test_catalog.py +++ b/tests/test_catalog.py @@ -1,7 +1,6 @@ from conftest import data_dir -from btk.catalog import CatsimCatalog -from btk.catalog import CosmosCatalog +from btk.catalog import CatsimCatalog, CosmosCatalog CATALOG_PATH = str(data_dir / "sample_input_catalog.fits") COSMOS_CATALOG_PATHS = [ diff --git a/tests/test_error_cases.py b/tests/test_error_cases.py index 4bd2fec97..af4a4a3a1 100644 --- a/tests/test_error_cases.py +++ b/tests/test_error_cases.py @@ -1,19 +1,21 @@ import pytest from conftest import data_dir -from btk.catalog import CatsimCatalog -from btk.catalog import CosmosCatalog -from btk.draw_blends import CatsimGenerator -from btk.draw_blends import CosmosGenerator -from btk.draw_blends import get_catsim_galaxy -from btk.draw_blends import SourceNotVisible -from btk.sampling_functions import DefaultSampling -from btk.sampling_functions import SamplingFunction -from btk.survey import Filter -from btk.survey import get_default_psf -from btk.survey import get_default_psf_with_galcheat_info -from btk.survey import get_psf_from_file -from btk.survey import get_surveys +from btk.catalog import CatsimCatalog, CosmosCatalog +from btk.draw_blends import ( + CatsimGenerator, + CosmosGenerator, + SourceNotVisible, + get_catsim_galaxy, +) +from btk.sampling_functions import DefaultSampling, SamplingFunction +from btk.survey import ( + Filter, + get_default_psf, + get_default_psf_with_galcheat_info, + get_psf_from_file, + get_surveys, +) CATALOG_PATH = data_dir / "sample_input_catalog.fits" diff --git a/tests/test_group_sampling.py b/tests/test_group_sampling.py deleted file mode 100644 index 9676c5203..000000000 --- a/tests/test_group_sampling.py +++ /dev/null @@ -1,49 +0,0 @@ -import numpy as np -from conftest import data_dir - -from btk.catalog import CatsimCatalog -from btk.draw_blends import CatsimGenerator -from btk.sampling_functions import GroupSamplingNumbered -from btk.survey import get_surveys - -TEST_SEED = 0 - - -def get_group_sampling_draw_generator(batch_size=3): - """Returns draw generator with group sampling function.""" - wld_catalog_name = data_dir / "sample_group_catalog.fits" - catalog_name = data_dir / "sample_group_input_catalog.fits" - - max_number = 10 - stamp_size = 24 - survey = get_surveys("LSST") - pixel_scale = 0.2 - shift = [0.8, -0.7] - catalog = CatsimCatalog.from_file(catalog_name) - sampling_function = GroupSamplingNumbered( - max_number, wld_catalog_name, stamp_size, pixel_scale, shift=shift, seed=TEST_SEED - ) - draw_blend_generator = CatsimGenerator( - catalog, sampling_function, [survey], batch_size=batch_size, seed=TEST_SEED - ) - return draw_blend_generator - - -def test_group_sampling(): - """Test blends drawn with group sampling function.""" - draw_blend_generator = get_group_sampling_draw_generator() - output = next(draw_blend_generator) - blend_images = output["blend_images"] - batch_max = blend_images.max(axis=(0, 2, 3)) - batch_mean = blend_images.mean() - batch_std = blend_images.std() - test_batch_max = np.array([13e2, 13e3, 43e3, 45e3, 30e3, 17e3]) - test_batch_mean = 82.1 - test_batch_std = 1027.6 - - rel_diff1 = (test_batch_max - batch_max) / test_batch_max - rel_diff2 = (batch_mean - test_batch_mean) / test_batch_mean - rel_diff3 = (batch_std - test_batch_std) / test_batch_std - assert np.all(rel_diff1 <= 0.15) - assert np.all(rel_diff2 <= 0.15) - assert np.all(rel_diff3 <= 0.15) diff --git a/tests/test_measure.py b/tests/test_measure.py index 88bbce8f3..fabe415f7 100644 --- a/tests/test_measure.py +++ b/tests/test_measure.py @@ -3,9 +3,7 @@ from btk.catalog import CatsimCatalog from btk.draw_blends import CatsimGenerator -from btk.measure import basic_measure -from btk.measure import MeasureGenerator -from btk.measure import sep_measure +from btk.measure import MeasureGenerator, basic_measure, sep_measure from btk.sampling_functions import DefaultSampling from btk.survey import get_surveys diff --git a/tests/test_metrics.py b/tests/test_metrics.py index b9d2ef4ca..f34270f53 100644 --- a/tests/test_metrics.py +++ b/tests/test_metrics.py @@ -6,16 +6,16 @@ import btk.plot_utils as plot_utils from btk.catalog import CatsimCatalog from btk.draw_blends import CatsimGenerator -from btk.measure import MeasureGenerator -from btk.measure import sep_measure -from btk.metrics import auc -from btk.metrics import get_detection_eff_matrix -from btk.metrics import meas_ksb_ellipticity -from btk.metrics import MetricsGenerator +from btk.measure import MeasureGenerator, sep_measure +from btk.metrics import ( + MetricsGenerator, + auc, + get_detection_eff_matrix, + meas_ksb_ellipticity, +) from btk.sampling_functions import DefaultSampling from btk.survey import get_surveys - TEST_SEED = 0 diff --git a/tests/test_mr.py b/tests/test_mr.py index 316e1d548..0a185b436 100644 --- a/tests/test_mr.py +++ b/tests/test_mr.py @@ -4,10 +4,8 @@ from btk.catalog import CatsimCatalog from btk.draw_blends import CatsimGenerator -from btk.measure import MeasureGenerator -from btk.measure import sep_measure -from btk.metrics import meas_ksb_ellipticity -from btk.metrics import MetricsGenerator +from btk.measure import MeasureGenerator, sep_measure +from btk.metrics import MetricsGenerator, meas_ksb_ellipticity from btk.plot_utils import plot_metrics_summary from btk.sampling_functions import DefaultSampling from btk.survey import get_surveys diff --git a/tests/test_save.py b/tests/test_save.py index cfc342ae3..104204de6 100644 --- a/tests/test_save.py +++ b/tests/test_save.py @@ -4,10 +4,8 @@ from btk.catalog import CatsimCatalog from btk.draw_blends import CatsimGenerator -from btk.measure import MeasureGenerator -from btk.measure import sep_measure -from btk.metrics import meas_ksb_ellipticity -from btk.metrics import MetricsGenerator +from btk.measure import MeasureGenerator, sep_measure +from btk.metrics import MetricsGenerator, meas_ksb_ellipticity from btk.sampling_functions import DefaultSampling from btk.survey import get_surveys from btk.utils import load_all_results