diff --git a/CITATIONS.rst b/CITATIONS.rst index d364f50c..7ae675ac 100644 --- a/CITATIONS.rst +++ b/CITATIONS.rst @@ -4,9 +4,9 @@ Citations & References ====================== The bibtex entries for **PyAutoCTI** and its affiliated software packages can be found -`here `_, with example text for citing **PyAutoCTI** -in `.tex format here `_ format here and -`.md format here `_. +`here `_, with example text for citing **PyAutoCTI** +in `.tex format here `_ format here and +`.md format here `_. As shown in the examples, we would greatly appreciate it if you mention **PyAutoCTI** by name and include a link to our GitHub page! diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index c5ac462d..77acd6b7 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -301,7 +301,7 @@ the situation is not yet resolved. ## License -This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://github.com/numfocus/numfocus/blob/master/manual/numfocus-coc.md#the-short-version), -which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/master/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/master/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct). +This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://github.com/numfocus/numfocus/blob/main/manual/numfocus-coc.md#the-short-version), +which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/main/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/main/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct). **PyAutoCTI Code of Conduct is licensed under the [Creative Commons Attribution 3.0 Unported License](https://creativecommons.org/licenses/by/3.0/).** \ No newline at end of file diff --git a/README.rst b/README.rst index 1b8aaf76..a1d52521 100644 --- a/README.rst +++ b/README.rst @@ -7,13 +7,17 @@ PyAutoCTI: Charge Transfer Inefficiency Modeling .. |binder| image:: https://mybinder.org/badge_logo.svg :target: https://mybinder.org/v2/gh/Jammy2211/autocti_workspace/HEAD +.. |RTD| image:: https://readthedocs.org/projects/pyautocti/badge/?version=latest + :target: https://pyautocti.readthedocs.io/en/latest/?badge=latest + :alt: Documentation Status + .. |code-style| image:: https://img.shields.io/badge/code%20style-black-000000.svg :target: https://github.com/psf/black .. |arXiv| image:: https://img.shields.io/badge/arXiv-1708.07377-blue :target: https://arxiv.org/abs/0909.0507 -|binder| |code-style| |arXiv| +|binder| |RTD| |code-style| |arXiv| `Installation Guide `_ | `readthedocs `_ | @@ -22,11 +26,11 @@ PyAutoCTI: Charge Transfer Inefficiency Modeling Charge Transfer Inefficiency, or CTI for short, is an effect that occurs when acquiring imaging data from Charge Coupled Devices (CCDs). Due to radiation damage to the CCD's silicon lattice electrons are read-out inefficiently, -creating a characterstic trailing or smearing effect. +creating a characteristic trailing or smearing effect. Here is an example of CTI in the Hubble space telescope, after decades of radiation damage: -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/what_is_cti.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/what_is_cti.png :width: 600 :alt: Alternative text diff --git a/autocti/instruments/acs/array_2d.py b/autocti/instruments/acs/array_2d.py index c5595f01..04d53f05 100644 --- a/autocti/instruments/acs/array_2d.py +++ b/autocti/instruments/acs/array_2d.py @@ -21,7 +21,7 @@ class Array2DACS(Array2D): """ An ACS array consists of four quadrants ('A', 'B', 'C', 'D') which have the following layout (which are described at the following STScI - link https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418). + link https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418). <--------S----------- ---------S-----------> [] [========= 2 =========] [========= 3 =========] [] /\ @@ -48,7 +48,7 @@ def from_fits(cls, file_path, quadrant_letter): See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and rotations. - Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 + Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 """ hdu = acs_util.fits_hdu_via_quadrant_letter_from( @@ -75,7 +75,7 @@ def from_ccd( See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and rotations. - Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 + Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 """ if quadrant_letter == "A": @@ -146,7 +146,7 @@ def quadrant_a( See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and rotations. - Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 + Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 """ array_electrons = layout_util.rotate_array_via_roe_corner_from( @@ -192,7 +192,7 @@ def quadrant_b( See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and rotations. - Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 + Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 """ array_electrons = layout_util.rotate_array_via_roe_corner_from( @@ -236,7 +236,7 @@ def quadrant_c( See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and rotations. - Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 + Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 """ array_electrons = layout_util.rotate_array_via_roe_corner_from( @@ -276,7 +276,7 @@ def quadrant_d( See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and rotations. - Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 + Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 """ array_electrons = layout_util.rotate_array_via_roe_corner_from( diff --git a/autocti/instruments/acs/image.py b/autocti/instruments/acs/image.py index 1dcaaf59..9068b554 100644 --- a/autocti/instruments/acs/image.py +++ b/autocti/instruments/acs/image.py @@ -41,7 +41,7 @@ def from_fits( See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and rotations. - Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 + Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418 Parameters ---------- diff --git a/docs/general/citations.rst b/docs/general/citations.rst index d364f50c..7ae675ac 100644 --- a/docs/general/citations.rst +++ b/docs/general/citations.rst @@ -4,9 +4,9 @@ Citations & References ====================== The bibtex entries for **PyAutoCTI** and its affiliated software packages can be found -`here `_, with example text for citing **PyAutoCTI** -in `.tex format here `_ format here and -`.md format here `_. +`here `_, with example text for citing **PyAutoCTI** +in `.tex format here `_ format here and +`.md format here `_. As shown in the examples, we would greatly appreciate it if you mention **PyAutoCTI** by name and include a link to our GitHub page! diff --git a/docs/index.rst b/docs/index.rst index bb0c7711..4e4cac67 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -7,9 +7,8 @@ Coupled Devices (CCDs). Lets take a look at a extract of data taken from the Advanced Camera for Surveys (ACS) instrument on board the Hubble Space Telescope (this figure is taken from Massey et al 2009 ``https://arxiv.org/abs/1009.4335``): -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/what_is_cti.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/what_is_cti.png :width: 600 - :alt: Alternative text Trailing -------- @@ -48,7 +47,7 @@ massive over simplification, but in order to understand CTI this process can be The animation below shows this process in action: -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/cti.gif +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/cti.gif :width: 600 CTI @@ -66,7 +65,7 @@ electron, one of two things can happen: The animation below shows the CCD clocking process, but now includes one of these traps: -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/ccd.gif +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/ccd.gif :width: 600 Charge Transfer diff --git a/docs/overview/overview_1_what_is_cti.rst b/docs/overview/overview_1_what_is_cti.rst index 37c675b4..329dc1dd 100644 --- a/docs/overview/overview_1_what_is_cti.rst +++ b/docs/overview/overview_1_what_is_cti.rst @@ -9,7 +9,7 @@ Coupled Devices (CCDs). Lets take a look at a extract of data taken from the Advanced Camera for Surveys (ACS) instrument on board the Hubble Space Telescope (this figure is taken from Massey et al 2009 ``https://arxiv.org/abs/1009.4335``): -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/what_is_cti.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/what_is_cti.png :width: 600 :alt: Alternative text @@ -42,7 +42,7 @@ massive over simplification, but in order to understand CTI this process can be The animation below shows this process in action: -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/cti.gif +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/cti.gif :width: 600 CTI @@ -60,7 +60,7 @@ electron, one of two things can happen: The animation below shows the CCD clocking process, but now includes one of these traps: -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/ccd.gif +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/ccd.gif :width: 600 Charge Transfer @@ -101,7 +101,7 @@ library has numerous wrappers like this which will crop up throughout the overvi array_1d_plotter = aplt.Array1DPlotter(y=pre_cti_data_1d) array_1d_plotter.figure_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_1/array_1d.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_1/array_1d.png :width: 600 :alt: Alternative text @@ -163,7 +163,7 @@ Note that, in 1D, clocking is to the left of the image. array_1d_plotter = aplt.Array1DPlotter(y=post_cti_data_1d) array_1d_plotter.figure_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_1/array_1d_with_cti.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_1/array_1d_with_cti.png :width: 600 :alt: Alternative text @@ -194,7 +194,7 @@ above, alongside the CTI model used to create it. array_1d_plotter = aplt.Array1DPlotter(y=corrected_cti_data_1d) array_1d_plotter.figure_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_1/array_1d_cti_corrected.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_1/array_1d_cti_corrected.png :width: 600 :alt: Alternative text @@ -224,7 +224,7 @@ traps. The longer our telescope has been in space, the more radiation will have have formed. The figure below slows the level of CTI in Hubble over the course of its lifetime -- as a function of time, CTI increases. -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/cti_time_evolution.gif +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/cti_time_evolution.gif :width: 600 Wrap Up diff --git a/docs/overview/overview_2_parallel_and_serial.rst b/docs/overview/overview_2_parallel_and_serial.rst index e7d2d5c0..1356229d 100644 --- a/docs/overview/overview_2_parallel_and_serial.rst +++ b/docs/overview/overview_2_parallel_and_serial.rst @@ -19,7 +19,7 @@ the image below) interspersed around regions with no charge. (It turns out that charge injection images are crucial to calibrating CTI -- a process we have to undertake before we can correct CTI in data. We cover this in overviews 4 and 5!). -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/ccd_schematic.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/ccd_schematic.png :width: 600 :alt: Alternative text @@ -97,7 +97,7 @@ with functionality used by **PyAutoCTI** which is expanded upon elsewhere in the array_2d_plotter = aplt.Array2DPlotter(array=pre_cti_data_2d) array_2d_plotter.figure_2d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/pre_cti_data_2d.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/pre_cti_data_2d.png :width: 600 :alt: Alternative text @@ -148,7 +148,7 @@ block of 10 electrons. array_2d_plotter = aplt.Array2DPlotter(array=post_cti_data_2d) array_2d_plotter.figure_2d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/post_cti_data_2d_parallel.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/post_cti_data_2d_parallel.png :width: 600 :alt: Alternative text @@ -191,7 +191,7 @@ block of 10 electrons. array_2d_plotter = aplt.Array2DPlotter(array=post_cti_data_2d) array_2d_plotter.figure_2d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/post_cti_data_2d_serial.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/post_cti_data_2d_serial.png :width: 600 :alt: Alternative text @@ -220,7 +220,7 @@ parallel CTI trails then trailed during serial clocking. array_2d_plotter = aplt.Array2DPlotter(array=post_cti_data_2d) array_2d_plotter.figure_2d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/post_cti_data_2d_parallel_serial.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/post_cti_data_2d_parallel_serial.png :width: 600 :alt: Alternative text @@ -236,7 +236,7 @@ Correcting CTI in 2D is as easy as it was in 1D, by simply calling the clockers array_2d_plotter = aplt.Array2DPlotter(array=corrected_cti_image_2d) array_2d_plotter.figure_2d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/post_cti_data_2d_corrected.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/post_cti_data_2d_corrected.png :width: 600 :alt: Alternative text diff --git a/docs/overview/overview_3_cti_features.rst b/docs/overview/overview_3_cti_features.rst index 7177d82b..a3facd34 100644 --- a/docs/overview/overview_3_cti_features.rst +++ b/docs/overview/overview_3_cti_features.rst @@ -59,11 +59,11 @@ Now lets plot the two datasets and compare their appearance. array_1d_plotter = aplt.Array1DPlotter(y=post_cti_data_1d_1) array_1d_plotter.figure_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/density_1.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/density_1.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/density_2.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/density_2.png :width: 600 :alt: Alternative text @@ -121,11 +121,11 @@ Now lets plot the two datasets and compare their appearance. array_1d_plotter = aplt.Array1DPlotter(y=post_cti_data_1d_1) array_1d_plotter.figure_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/timescale_1.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/timescale_1.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/timescale_2.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/timescale_2.png :width: 600 :alt: Alternative text @@ -208,10 +208,10 @@ We can illustrate this by comparing the addition of CTI to two 1D datasets with array_1d_plotter = aplt.Array1DPlotter(y=post_cti_data_1d_1) array_1d_plotter.figure_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/volume_1.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/volume_1.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/volume_2.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/volume_2.png :width: 600 :alt: Alternative text \ No newline at end of file diff --git a/docs/overview/overview_4_charge_injection_data.rst b/docs/overview/overview_4_charge_injection_data.rst index 5fd836c7..f63ce2d0 100644 --- a/docs/overview/overview_4_charge_injection_data.rst +++ b/docs/overview/overview_4_charge_injection_data.rst @@ -10,7 +10,7 @@ of a dataset, lets consider how a charge injection dataset contains everything w Lets again load our 2D schematic of a charge injection image: -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/ccd_schematic.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/ccd_schematic.png :width: 600 :alt: Alternative text @@ -115,7 +115,7 @@ We can plot the charge injection imaging using a ``ImagingCI`` object. imaging_ci_plotter = aplt.ImagingCIPlotter(imaging=imaging_ci) imaging_ci_plotter.figures_2d(image=True) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_4/imaging_ci.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_4/imaging_ci.png :width: 600 :alt: Alternative text @@ -140,7 +140,7 @@ We can zoom in on one of these regions and change the color scheme to properly h imaging_ci_plotter = aplt.ImagingCIPlotter(imaging=imaging_ci, mat_plot_2d=mat_plot_2d) imaging_ci_plotter.figures_2d(image=True) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_4/imaging_ci_fpr.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_4/imaging_ci_fpr.png :width: 600 :alt: Alternative text @@ -156,7 +156,7 @@ We can do the same to highlight the EPERs. imaging_ci_plotter = aplt.ImagingCIPlotter(imaging=imaging_ci, mat_plot_2d=mat_plot_2d) imaging_ci_plotter.figures_2d(image=True) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_4/imaging_ci_eper.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_4/imaging_ci_eper.png :width: 600 :alt: Alternative text @@ -174,7 +174,7 @@ every parallel EPERs binned together. array_1d_plotter = aplt.Array1DPlotter(y=parallel_eper_1d) array_1d_plotter.figure_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_4/parallel_eper_binned.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_4/parallel_eper_binned.png :width: 600 :alt: Alternative text @@ -200,15 +200,15 @@ The layout can extract all the regions of interest of the data. array_1d_plotter = aplt.Array1DPlotter(y=serial_fpr_1d) array_1d_plotter.figure_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_4/parallel_fpr_binned.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_4/parallel_fpr_binned.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_4/serial_eper_binned.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_4/serial_eper_binned.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_4/serial_fpr_binned.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_4/serial_fpr_binned.png :width: 600 :alt: Alternative text @@ -223,7 +223,7 @@ contained in the ``pre_cti_data``. imaging_ci_plotter = aplt.ImagingCIPlotter(imaging=imaging_ci, mat_plot_2d=mat_plot_2d) imaging_ci_plotter.figures_2d(pre_cti_data=True) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_4/pre_cti_data.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_4/pre_cti_data.png :width: 600 :alt: Alternative text @@ -264,7 +264,7 @@ More realistic charge injection imaging has many other features, for example: imaging_ci_plotter = aplt.ImagingCIPlotter(imaging=imaging_ci) imaging_ci_plotter.figures_2d(image=True, pre_cti_data=True) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_4/imaging_ci_non_uniform_cosmic_rays.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_4/imaging_ci_non_uniform_cosmic_rays.png :width: 600 :alt: Alternative text diff --git a/docs/overview/overview_5_fitting.rst b/docs/overview/overview_5_fitting.rst index c992284d..b82be4d2 100644 --- a/docs/overview/overview_5_fitting.rst +++ b/docs/overview/overview_5_fitting.rst @@ -76,11 +76,11 @@ CTI is straightforward. imaging_ci_plotter = aplt.ImagingCIPlotter(imaging=imaging_ci) imaging_ci_plotter.figures_2d(image=True, pre_cti_data=True) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/image.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/image.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/pre_cti_data.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/pre_cti_data.png :width: 600 :alt: Alternative text @@ -146,15 +146,15 @@ indicating a bad model fit. residual_map=True, normalized_residual_map=True, chi_squared_map=True ) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/residual_map.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/residual_map.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/normalized_residual_map.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/normalized_residual_map.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/chi_squared_map.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/chi_squared_map.png :width: 600 :alt: Alternative text @@ -204,15 +204,15 @@ The plot of the residuals now shows no significant signal, indicating a good fit residual_map=True, normalized_residual_map=True, chi_squared_map=True ) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/residual_map_good.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/residual_map_good.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/normalized_residual_map_good.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/normalized_residual_map_good.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/chi_squared_map_good.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/chi_squared_map_good.png :width: 600 :alt: Alternative text @@ -256,7 +256,7 @@ If we apply this mask to the charge injection imaging and plot it, the parallel imaging_ci_plotter = aplt.ImagingCIPlotter(imaging=imaging_ci) imaging_ci_plotter.figures_2d(image=True) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/image_masked.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/image_masked.png :width: 600 :alt: Alternative text @@ -272,15 +272,15 @@ map are masked and not included in the fit. residual_map=True, normalized_residual_map=True, chi_squared_map=True ) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/residual_map_masked.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/residual_map_masked.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/normalized_residual_map_masked.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/normalized_residual_map_masked.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/chi_squared_map_masked.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/chi_squared_map_masked.png :width: 600 :alt: Alternative text @@ -333,11 +333,11 @@ injection data. dataset_1d_plotter = aplt.Dataset1DPlotter(dataset=dataset_1d) dataset_1d_plotter.subplot_dataset_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/data_1d.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/data_1d.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/pre_cti_data_1d.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/pre_cti_data_1d.png :width: 600 :alt: Alternative text @@ -387,15 +387,15 @@ Plotting the fit shows this model gives a good fit, with minimal residuals. residual_map=True, normalized_residual_map=True, chi_squared_map=True ) -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/residual_map_1d.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/residual_map_1d.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/normalized_residual_map_1d.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/normalized_residual_map_1d.png :width: 600 :alt: Alternative text -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_5/chi_squared_map_1d.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_5/chi_squared_map_1d.png :width: 600 :alt: Alternative text diff --git a/docs/overview/overview_6_cti_calibration.rst b/docs/overview/overview_6_cti_calibration.rst index 6844a712..28345a35 100644 --- a/docs/overview/overview_6_cti_calibration.rst +++ b/docs/overview/overview_6_cti_calibration.rst @@ -284,7 +284,7 @@ Below, we plot a subplot of the fit for the first dataset which shows a good fit fit_plotter = aplt.FitImagingCIPlotter(fit=result_list[0].max_log_likelihood_fit) fit_plotter.subplot_fit_ci() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_6/fit_2d_100.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_6/fit_2d_100.png :width: 600 :alt: Alternative text @@ -416,7 +416,7 @@ maximum likelihood fit. fit_plotter = aplt.FitDataset1DPlotter(fit=result.max_log_likelihood_fit) fit_plotter.subplot_fit_dataset_1d() -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_6/fit_1d_100.png +.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_6/fit_1d_100.png :width: 600 :alt: Alternative text diff --git a/setup.py b/setup.py index 184564f6..62f3755c 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ version=version, description="PyAutoCTI: Charge Transfer Inefficiency Modeling", long_description=long_description, - long_description_content_type="text/markdown", + long_description_content_type="text/x-rst", url="https://github.com/jammy2211/PyAutoCTI", author="James Nightingale, Richard Massey, Jacob Kegerreis and Richard Hayes", author_email="james.w.nightingale@durham.ac.uk",