From 0e1a7d182c0e70a02e8fc6e3b119dafe94ce706b Mon Sep 17 00:00:00 2001 From: troyraen Date: Sun, 11 Feb 2024 03:18:41 -0800 Subject: [PATCH] drop figures module. drop aplpy, matplotlib, numpy dependencies. add tutorial ztf-figures. update changelog. --- CHANGELOG.md | 9 +- docs/source/api/figures.rst | 5 - docs/source/index.rst | 2 +- docs/source/tutorials/bigquery.rst | 31 +- docs/source/tutorials/cloud-storage.rst | 29 +- docs/source/tutorials/ztf-figures.rst | 137 +++ pittgoogle/__init__.py | 2 +- pittgoogle/figures.py | 130 --- poetry.lock | 1013 +---------------------- pyproject.toml | 3 - 10 files changed, 177 insertions(+), 1184 deletions(-) delete mode 100644 docs/source/api/figures.rst create mode 100644 docs/source/tutorials/ztf-figures.rst delete mode 100644 pittgoogle/figures.py diff --git a/CHANGELOG.md b/CHANGELOG.md index 9bf4dd1..862c2cd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,11 +10,19 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) ## \[Unreleased\] +### Added + +- ZTF Figures Tutorial + ### Changed - update README.md to point to the new docs - remove setup and requirements files that are no longer needed after switching away from Read The Docs +### Removed + +- `figures` module (content moved to tutorial). This allowed the removal of the following explicit dependencies: `aplpy`, `matplotlib`, `numpy`. + ## \[0.2.0\] - 2023-07-02 ### Added @@ -33,4 +41,3 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) ### Fixed - cleanup some issues flagged by Codacy - diff --git a/docs/source/api/figures.rst b/docs/source/api/figures.rst deleted file mode 100644 index 1b1c083..0000000 --- a/docs/source/api/figures.rst +++ /dev/null @@ -1,5 +0,0 @@ -pittgoogle.figures -=================== - -.. automodule:: pittgoogle.figures - :members: diff --git a/docs/source/index.rst b/docs/source/index.rst index 20bc2b1..e17ab2f 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -21,6 +21,7 @@ tutorials/bigquery tutorials/cloud-storage + tutorials/ztf-figures .. toctree:: :caption: API Reference @@ -29,7 +30,6 @@ api/auth api/bigquery - api/figures api/pubsub api/utils diff --git a/docs/source/tutorials/bigquery.rst b/docs/source/tutorials/bigquery.rst index f2a0181..ff21e73 100644 --- a/docs/source/tutorials/bigquery.rst +++ b/docs/source/tutorials/bigquery.rst @@ -1,3 +1,5 @@ +.. _bigquery: + BigQuery Tutorial ================== @@ -77,13 +79,13 @@ It's options are demonstrated below. # Option 1: Get a single DataFrame of all results - lcs_df = pittgoogle.bigquery.query_objects(columns, objectIds=objectIds) + lightcurves_df = pittgoogle.bigquery.query_objects(columns, objectIds=objectIds) # This will execute a dry run and tell you how much data will be processed. # You will be asked to confirm before proceeding. # In the future we'll skip this using dry_run = False - lcs_df.sample(10) + lightcurves_df.sample(10) # cleaned of duplicates Congratulations! You've now retrieved your first data from the transient @@ -101,8 +103,8 @@ common name in the table schema we looked at earlier, or you can use fid_names = pittgoogle.utils.ztf_fid_names() # dict print(fid_names) - lcs_df['filter'] = lcs_df['fid'].map(fid_names) - lcs_df.head() + lightcurves_df['filter'] = lightcurves_df['fid'].map(fid_names) + lightcurves_df.head() Queries can return large datasets. You may want to use a generator to step through objects individually, and avoid loading the entire dataset @@ -118,9 +120,9 @@ into memory at once. ``query_objects()`` can return one for you: ) # cleaned of duplicates - for lc_df in objects: - print(f'\nobjectId: {lc_df.objectId}') # objectId in metadata - print(lc_df.sample(5)) + for lightcurve_df in objects: + print(f'\nobjectId: {lightcurve_df.objectId}') # objectId in metadata + print(lightcurve_df.sample(5)) Each DataFrame contains data on a single object, and is indexed by ``candid``. The ``objectId`` is in the metadata. @@ -156,7 +158,7 @@ results: for lcjson in jobj: print(lcjson) - # lc_df = pd.read_json(lcjson) # read back to a df + # lightcurve_df = pd.read_json(lcjson) # read back to a df Finally, ``query_objects()`` can return the raw query job object that it gets from its API call using ``google.cloud.bigquery``'s ``query()`` @@ -184,9 +186,9 @@ method. # pgb can cast to a DataFrame or json string # this option also cleans the duplicates - lc_df = pittgoogle.bigquery.format_history_query_results(row=row) - print(f'\nobjectId: {lc_df.objectId}') # objectId in metadata - print(lc_df.head(1)) + lightcurve_df = pittgoogle.bigquery.format_history_query_results(row=row) + print(f'\nobjectId: {lightcurve_df.objectId}') # objectId in metadata + print(lightcurve_df.head(1)) lcjson = pittgoogle.bigquery.format_history_query_results(row=row, format='json') print('\n', lcjson) @@ -195,15 +197,14 @@ method. Plot a lightcurve ^^^^^^^^^^^^^^^^^ +The following DataFrame can be used with the code in :ref:`ztf figures` to plot the object's light curves. + .. code:: python # Get an object's lightcurve DataFrame with the minimum required columns columns = ['jd','fid','magpsf','sigmapsf','diffmaglim'] objectId = 'ZTF20acqgklx' - lc_df = pittgoogle.bigquery.query_objects(columns, objectIds=[objectId], dry_run=False) - - # make the plot - pittgoogle.figures.plot_lightcurve(lc_df, objectId=objectId) + lightcurve_df = pittgoogle.bigquery.query_objects(columns, objectIds=[objectId], dry_run=False) Cone search ~~~~~~~~~~~ diff --git a/docs/source/tutorials/cloud-storage.rst b/docs/source/tutorials/cloud-storage.rst index 85c6214..5078804 100644 --- a/docs/source/tutorials/cloud-storage.rst +++ b/docs/source/tutorials/cloud-storage.rst @@ -1,3 +1,5 @@ +.. _cloud storage: + Cloud Storage Tutorial ============================== @@ -65,13 +67,10 @@ Download alerts for a given ``objectId`` blob.download_to_filename(local_path) print(f'Downloaded {local_path}') -Plot cutouts and lightcurves +Open a file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -The functions in this section were adapted from -https://github.com/ZwickyTransientFacility/ztf-avro-alert/blob/master/notebooks/Filtering\_alerts.ipynb. - -Open a file (see the previous section to download files) +Load to a dict: .. code:: python @@ -84,27 +83,17 @@ Open a file (see the previous section to download files) print(alert_dict.keys()) -Plot cutouts +Load to a pandas DataFrame: .. code:: python - pittgoogle.figures.plot_cutouts(alert_dict) - plt.show(block=False) + lightcurve_df = pittgoogle.utils.Cast.alert_dict_to_dataframe(alert_dict) -Cast to a dataframe and plot lightcurves - -.. code:: python - lc_df = pittgoogle.utils.Cast.alert_dict_to_dataframe(alert_dict) - pittgoogle.figures.plot_lightcurve(lc_df) - plt.show(block=False) - -Plot everything together - -.. code:: python +Plot light curves and cutouts +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - pittgoogle.figures.plot_lightcurve_cutouts(alert_dict) - plt.show(block=False) +See :ref:`ztf figures` Command line ------------ diff --git a/docs/source/tutorials/ztf-figures.rst b/docs/source/tutorials/ztf-figures.rst new file mode 100644 index 0000000..0ec8695 --- /dev/null +++ b/docs/source/tutorials/ztf-figures.rst @@ -0,0 +1,137 @@ +.. _ztf figures: + +ZTF Figures Tutorial +============================== + +.. contents:: Table of Contents + :depth: 1 + :local: + +This tutorial demonstrates plotting ZTF cutouts and light curves. +It is based heavily on https://github.com/ZwickyTransientFacility/ztf-avro-alert/blob/master/notebooks/Filtering_alerts.ipynb. + +Prerequisites +------------- + +1. Load a ZTF alert to a dict or a pandas DataFrame. For examples, see: + + - :ref:`cloud storage` + - :ref:`bigquery` + +Imports +--------- + +.. code:: python + + import gzip + import io + from typing import Optional + + import aplpy + import matplotlib as mpl + import numpy as np + import pandas as pd + from astropy.io import fits + from astropy.time import Time + from matplotlib import pyplot as plt + + import pittgoogle + +Plot a Light Curve +------------------ + +.. code:: python + + def plot_lightcurve(lightcurve_df: pd.DataFrame, days_ago: bool = True): + """Plot the per-band light curve of a single ZTF object. + Adapted from: + https://github.com/ZwickyTransientFacility/ztf-avro-alert/blob/master/notebooks/Filtering_alerts.ipynb + + Parameters + ---------- + lightcurve_df + Lightcurve history of a ZTF object. Must contain columns + ['jd','fid','magpsf','sigmapsf','diffmaglim'] + days_ago + If True, x-axis will be number of days in the past. + Else x-axis will be Julian date. + """ + + filter_code = pittgoogle.utils.ztf_fid_names() # dict + filter_color = {1: "green", 2: "red", 3: "pink"} + + # set the x-axis (time) details + if days_ago: + now = Time.now().jd + t = lightcurve_df.jd - now + xlabel = "Days Ago" + else: + t = lightcurve_df.jd + xlabel = "Time (JD)" + + # plot lightcurves by band + for fid, color in filter_color.items(): + # plot detections in this filter: + w = (lightcurve_df.fid == fid) & ~lightcurve_df.magpsf.isnull() + if np.sum(w): + label = f"{fid}: {filter_code[fid]}" + kwargs = {"fmt": ".", "color": color, "label": label} + plt.errorbar(t[w], lightcurve_df.loc[w, "magpsf"], lightcurve_df.loc[w, "sigmapsf"], **kwargs) + # plot nondetections in this filter + wnodet = (lightcurve_df.fid == fid) & lightcurve_df.magpsf.isnull() + if np.sum(wnodet): + plt.scatter( + t[wnodet], + lightcurve_df.loc[wnodet, "diffmaglim"], + marker="v", + color=color, + alpha=0.25, + ) + + plt.gca().invert_yaxis() + plt.xlabel(xlabel) + plt.ylabel("Magnitude") + plt.legend() + +.. code:: python + + plot_lightcurve(lightcurve_df) + +Plot Cutouts +------------ + +.. code:: python + + def plot_stamp(stamp, fig=None, subplot=None, **kwargs): + """Adapted from: + https://github.com/ZwickyTransientFacility/ztf-avro-alert/blob/master/notebooks/Filtering_alerts.ipynb + """ + + with gzip.open(io.BytesIO(stamp), "rb") as f: + with fits.open(io.BytesIO(f.read())) as hdul: + if fig is None: + fig = plt.figure(figsize=(4, 4)) + if subplot is None: + subplot = (1, 1, 1) + ffig = aplpy.FITSFigure(hdul[0], figure=fig, subplot=subplot, **kwargs) + ffig.show_grayscale(stretch="arcsinh") + return ffig + + + def plot_cutouts(alert_dict): + """Adapted from: + https://github.com/ZwickyTransientFacility/ztf-avro-alert/blob/master/notebooks/Filtering_alerts.ipynb + """ + + # fig, axes = plt.subplots(1,3, figsize=(12,4)) + fig = plt.figure(figsize=(12, 4)) + for i, cutout in enumerate(["Science", "Template", "Difference"]): + stamp = alert_dict["cutout{}".format(cutout)]["stampData"] + ffig = plot_stamp(stamp, fig=fig, subplot=(1, 3, i + 1)) + ffig.set_title(cutout) + + +.. code:: python + + plot_cutouts(alert_dict) + plt.show(block=False) diff --git a/pittgoogle/__init__.py b/pittgoogle/__init__.py index 61df91c..47238f1 100644 --- a/pittgoogle/__init__.py +++ b/pittgoogle/__init__.py @@ -9,7 +9,7 @@ except ImportError: # for Python<3.8 import importlib_metadata as metadata -from . import auth, bigquery, exceptions, figures, pubsub, utils +from . import auth, bigquery, exceptions, pubsub, utils __version__ = metadata.version("pittgoogle-client") diff --git a/pittgoogle/figures.py b/pittgoogle/figures.py deleted file mode 100644 index 7e8bead..0000000 --- a/pittgoogle/figures.py +++ /dev/null @@ -1,130 +0,0 @@ -# -*- coding: UTF-8 -*- -"""``figures`` contains functions for plotting alert and history data. -See the tutorials for usage help. -""" -# import gzip -# import io -from typing import Optional - -# import aplpy -import matplotlib as mpl -import numpy as np -import pandas as pd - -# from astropy.io import fits -from astropy.time import Time -from matplotlib import pyplot as plt - -from . import utils as pgbu - - -# --- Plot object history -def plot_lightcurve( - dflc: pd.DataFrame, - objectId: Optional[str] = None, - ax: Optional[mpl.axes.Axes] = None, - days_ago: bool = True, -): - """Plot the lighcurve (per band) of a single ZTF object. - Adapted from: - https://github.com/ZwickyTransientFacility/ztf-avro-alert/blob/master/notebooks/Filtering_alerts.ipynb - - Args: - dflc: Lightcurve history of a unique objectId. Must contain columns - ['jd','fid','magpsf','sigmapsf','diffmaglim'] - objectId: objectId identifying dflc. Used for plot title. - ax: matplotlib axes for the figure. If None, a new figure will be created - days_ago: If True, x-axis will be number of days in the past. - Else x-axis will be Julian date. - """ - - filter_code = pgbu.ztf_fid_names() # dict - filter_color = {1: "green", 2: "red", 3: "pink"} - - # set the x-axis (time) details - if days_ago: - now = Time.now().jd - t = dflc.jd - now - xlabel = "Days Ago" - else: - t = dflc.jd - xlabel = "Time (JD)" - - if ax is None: - plt.figure() - - # plot lightcurves by band - for fid, color in filter_color.items(): - # plot detections in this filter: - w = (dflc.fid == fid) & ~dflc.magpsf.isnull() - if np.sum(w): - label = f"{fid}: {filter_code[fid]}" - kwargs = {"fmt": ".", "color": color, "label": label} - plt.errorbar(t[w], dflc.loc[w, "magpsf"], dflc.loc[w, "sigmapsf"], **kwargs) - # plot nondetections in this filter - wnodet = (dflc.fid == fid) & dflc.magpsf.isnull() - if np.sum(wnodet): - plt.scatter( - t[wnodet], - dflc.loc[wnodet, "diffmaglim"], - marker="v", - color=color, - alpha=0.25, - ) - - plt.gca().invert_yaxis() - plt.xlabel(xlabel) - plt.ylabel("Magnitude") - plt.legend() - plt.title(f"objectId: {objectId}") - - -# --- Plot cutouts -# def plot_stamp(stamp, fig=None, subplot=None, **kwargs): -# """Adapted from: -# https://github.com/ZwickyTransientFacility/ztf-avro-alert/blob/master/notebooks/Filtering_alerts.ipynb -# """ - -# with gzip.open(io.BytesIO(stamp), "rb") as f: -# with fits.open(io.BytesIO(f.read())) as hdul: -# if fig is None: -# fig = plt.figure(figsize=(4, 4)) -# if subplot is None: -# subplot = (1, 1, 1) -# ffig = aplpy.FITSFigure(hdul[0], figure=fig, subplot=subplot, **kwargs) - -# # the following has been throwing: `ValueError: a must be > 0 and <= 1` -# # this is fixed by requiring astropy==3.2.1 -# # Note: I see this related thing: https://github.com/aplpy/aplpy/issues/420 -# # but I am using the latest APLpy version (2.0.3). -# # update (2023-06-26): this seems to be working now with astropy==5.2.2 -# ffig.show_grayscale(stretch="arcsinh") -# return ffig - - -# def plot_cutouts(alert_dict): -# """Adapted from: -# https://github.com/ZwickyTransientFacility/ztf-avro-alert/blob/master/notebooks/Filtering_alerts.ipynb -# """ - -# # fig, axes = plt.subplots(1,3, figsize=(12,4)) -# fig = plt.figure(figsize=(12, 4)) -# for i, cutout in enumerate(["Science", "Template", "Difference"]): -# stamp = alert_dict["cutout{}".format(cutout)]["stampData"] -# ffig = plot_stamp(stamp, fig=fig, subplot=(1, 3, i + 1)) -# ffig.set_title(cutout) - - -# # --- Plot all -# def plot_lightcurve_cutouts(alert_dict): -# """Adapted from: -# https://github.com/ZwickyTransientFacility/ztf-avro-alert/blob/master/notebooks/Filtering_alerts.ipynb -# """ - -# fig = plt.figure(figsize=(16, 4)) -# dflc = pgbu.Cast.alert_dict_to_dataframe(alert_dict) -# plot_lightcurve(dflc, ax=plt.subplot(1, 4, 1)) -# for i, cutout in enumerate(["Science", "Template", "Difference"]): -# stamp = alert_dict["cutout{}".format(cutout)]["stampData"] -# ffig = plot_stamp(stamp, fig=fig, subplot=(1, 4, i + 2)) -# ffig.set_title(cutout) diff --git a/poetry.lock b/poetry.lock index a337691..019809b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,42 +11,6 @@ files = [ {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] -[[package]] -name = "aplpy" -version = "2.1.0" -description = "The Astronomical Plotting Library in Python" -optional = false -python-versions = ">=3.6" -files = [ - 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