Fix images titles and arrangements in docs

README.md

@@ -1,4 +1,4 @@
-# <ins>Bi</ins>o <ins>R</ins>eactor <ins>D</ins>esign (BiRD) Toolbox [![bird-CI](https://github.com/NREL/BioReactorDesign/actions/workflows/ci.yml/badge.svg)](https://github.com/NREL/BioReactorDesign/actions/workflows/ci.yml) [![bird-pyversion](https://img.shields.io/pypi/pyversions/NREL-bird.svg)](https://pypi.org/project/NREL-bird/)  [![bird-pypi](https://badge.fury.io/py/nrel-bird.svg)](https://badge.fury.io/py/nrel-bird)
+# <ins>Bi</ins>o <ins>R</ins>eactor <ins>D</ins>esign (BiRD) [![bird-CI](https://github.com/NREL/BioReactorDesign/actions/workflows/ci.yml/badge.svg)](https://github.com/NREL/BioReactorDesign/actions/workflows/ci.yml) [![bird-pyversion](https://img.shields.io/pypi/pyversions/NREL-bird.svg)](https://pypi.org/project/NREL-bird/)  [![bird-pypi](https://badge.fury.io/py/nrel-bird.svg)](https://badge.fury.io/py/nrel-bird)
 
 ## Quick start
 1. Follow the steps to install the python package (see `Installation of python package for developers` or `Installation of python package for users` below)

docs/source/calibration.rst

@@ -43,7 +43,7 @@ The following plots should be generated. The first one shows the training and te
 .. container:: figures-surr-train
 
    .. figure:: ../assets/calibration/tutorial_normal_beta/Loss_surr.png
-      :width: 30%
+      :width: 50%
       :align: center
       :alt: Loss history
 
@@ -67,18 +67,16 @@ Calibrate without a surrogate for ``alpha=5, beta=5``
    python tut_calibration.py --alpha 5 --beta 5
 
 
-.. container:: figures-cal-True-5-5
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/True_opt_5.0_5.0_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the true forward model
+|figures-cal-True-5-5-prop| |figures-cal-True-5-5-corn|
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/True_opt_5.0_5.0_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the true forward model
+.. |figures-cal-True-5-5-prop| image:: ../assets/calibration/tutorial_normal_beta/True_opt_5.0_5.0_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the true forward model
 
+.. |figures-cal-True-5-5-corn| image:: ../assets/calibration/tutorial_normal_beta/True_opt_5.0_5.0_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the true forward model
 
 Calibrate with a surrogate for ``alpha=5, beta=5``
 
@@ -87,18 +85,15 @@ Calibrate with a surrogate for ``alpha=5, beta=5``
    python tut_calibration.py -useNN --alpha 5 --beta 5
 
 
+|figures-cal-Surr-5-5-prop| |figures-cal-Surr-5-5-corn|
 
-.. container:: figures-cal-Surr-5-5
+.. |figures-cal-Surr-5-5-prop| image:: ../assets/calibration/tutorial_normal_beta/Surr_opt_5.0_5.0_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the surrogate forward model
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/Surr_opt_5.0_5.0_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the surrogate forward model
-
-   .. figure:: ../assets/calibration/tutorial_normal_beta/Surr_opt_5.0_5.0_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the surrogate forward model
+.. |figures-cal-Surr-5-5-corn| image:: ../assets/calibration/tutorial_normal_beta/Surr_opt_5.0_5.0_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the surrogate forward model
 
 
 Calibrate without a surrogate for ``alpha=2, beta=5``
@@ -109,17 +104,15 @@ Calibrate without a surrogate for ``alpha=2, beta=5``
    python tut_calibration.py --alpha 2 --beta 5
 
 
-.. container:: figures-cal-True-2-5
+|figures-cal-True-2-5-prop| |figures-cal-True-2-5-corn|
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/True_opt_2.0_5.0_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the true forward model
+.. |figures-cal-True-2-5-prop| image:: ../assets/calibration/tutorial_normal_beta/True_opt_2.0_5.0_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the true forward model
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/True_opt_2.0_5.0_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the true forward model
+.. |figures-cal-True-2-5-corn| image:: ../assets/calibration/tutorial_normal_beta/True_opt_2.0_5.0_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the true forward model
 
 
 Calibrate with a surrogate for ``alpha=2, beta=5``
@@ -130,17 +123,15 @@ Calibrate with a surrogate for ``alpha=2, beta=5``
 
 
 
-.. container:: figures-cal-True-2-5
+|figures-cal-Surr-2-5-prop| |figures-cal-Surr-2-5-corn|
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/Surr_opt_2.0_5.0_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the surrogate forward model
+.. |figures-cal-Surr-2-5-prop| image:: ../assets/calibration/tutorial_normal_beta/Surr_opt_2.0_5.0_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the surrogate forward model
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/Surr_opt_2.0_5.0_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the surrogate forward model
+.. |figures-cal-Surr-2-5-corn| image:: ../assets/calibration/tutorial_normal_beta/Surr_opt_2.0_5.0_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the surrogate forward model
 
 
 Clearly, the amount of missing physics vary depending on the observations.
@@ -160,17 +151,15 @@ Calibrate without a surrogate for ``alpha=5, beta=5``
    python tut_calibration.py --alpha 5 --beta 5 -cal_err
 
 
-.. container:: figures-cal-calerr-True-5-5
+|figures-cal-calerr-True-5-5-prop| |figures-cal-calerr-True-5-5-corn|
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/True_cal_5.0_5.0_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the true forward model
+.. |figures-cal-calerr-True-5-5-prop| image:: ../assets/calibration/tutorial_normal_beta/True_cal_5.0_5.0_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the true forward model
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/True_cal_5.0_5.0_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the true forward model
+.. |figures-cal-calerr-True-5-5-corn| image:: ../assets/calibration/tutorial_normal_beta/True_cal_5.0_5.0_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the true forward model
 
 
 Calibrate with a surrogate for ``alpha=5, beta=5``
@@ -180,18 +169,15 @@ Calibrate with a surrogate for ``alpha=5, beta=5``
    python tut_calibration.py -useNN --alpha 5 --beta 5 -cal_err
 
 
+|figures-cal-calerr-Surr-5-5-prop| |figures-cal-calerr-Surr-5-5-corn|
 
-.. container:: figures-cal-calerr-Surr-5-5
+.. |figures-cal-calerr-Surr-5-5-prop| image:: ../assets/calibration/tutorial_normal_beta/Surr_cal_5.0_5.0_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the surrogate forward model
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/Surr_cal_5.0_5.0_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the surrogate forward model
-
-   .. figure:: ../assets/calibration/tutorial_normal_beta/Surr_cal_5.0_5.0_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the surrogate forward model
+.. |figures-cal-calerr-Surr-5-5-corn| image:: ../assets/calibration/tutorial_normal_beta/Surr_cal_5.0_5.0_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the surrogate forward model
 
 
 Calibrate without a surrogate for ``alpha=2, beta=5``
@@ -202,17 +188,15 @@ Calibrate without a surrogate for ``alpha=2, beta=5``
    python tut_calibration.py --alpha 2 --beta 5 -cal_err
 
 
-.. container:: figures-cal-calerr-True-2-5
+|figures-cal-calerr-True-2-5-prop| |figures-cal-calerr-True-2-5-corn|
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/True_cal_2.0_5.0_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the true forward model
+.. |figures-cal-calerr-True-2-5-prop| image:: ../assets/calibration/tutorial_normal_beta/True_cal_2.0_5.0_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the true forward model
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/True_cal_2.0_5.0_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the true forward model
+.. |figures-cal-calerr-True-2-5-corn| image:: ../assets/calibration/tutorial_normal_beta/True_cal_2.0_5.0_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the true forward model
 
 
 Calibrate with a surrogate for ``alpha=2, beta=5``
@@ -223,17 +207,16 @@ Calibrate with a surrogate for ``alpha=2, beta=5``
 
 
 
-.. container:: figures-cal-calerr-True-2-5
+|figures-cal-calerr-Surr-2-5-prop| |figures-cal-calerr-Surr-2-5-corn|
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/Surr_cal_2.0_5.0_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the surrogate forward model
+.. |figures-cal-calerr-Surr-2-5-prop| image:: ../assets/calibration/tutorial_normal_beta/Surr_cal_2.0_5.0_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the surrogate forward model
+
+.. |figures-cal-calerr-Surr-2-5-corn| image:: ../assets/calibration/tutorial_normal_beta/Surr_cal_2.0_5.0_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the surrogate forward model
 
-   .. figure:: ../assets/calibration/tutorial_normal_beta/Surr_cal_2.0_5.0_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the surrogate forward model
 
 
 

docs/source/calibration_bsd.rst

@@ -94,33 +94,28 @@ The plot below shows the values of `Bf` and `Cr` simulated and whether they lead
 
 We can also look at how close the generated data is to the target data. For the ternary breakup and coalescence, there is clearly a discrepancy that is not resolvable by adjusting the coalescence and breakup rates.
 
+|figures-viz-pred-ter_bf| |figures-viz-pred-ter_cr|
 
-.. container:: figures-viz-pred-ter
+.. |figures-viz-pred-ter_bf| image:: ../assets/calibration/tutorial_bsd/cmap_bf_ternary.png
+   :width: 49.5%
+   :alt: Predicted data with the binary breakup and coalescence colored by Bf against the ternary target data
 
-   .. figure:: ../assets/calibration/tutorial_bsd/cmap_bf_ternary.png
-      :width: 50%
-      :align: center
-      :alt: Predicted data with the binary breakup and coalescence colored by Bf against the ternary target data
-
-   .. figure:: ../assets/calibration/tutorial_bsd/cmap_cr_ternary.png
-      :width: 50%
-      :align: center
-      :alt: Predicted data with the binary breakup and coalescence colored by Cr against the ternary target data
+.. |figures-viz-pred-ter_cr| image:: ../assets/calibration/tutorial_bsd/cmap_cr_ternary.png
+   :width: 49.5%
+   :alt: Predicted data with the binary breakup and coalescence colored by Cr against the ternary target data
 
 
 In the case of the binary breakup and coalescence target data, a low value of `Bf` and a high value of `Cr` should lead to a good agreement between the forward model and the target data.
 
-.. container:: figures-viz-pred-bin
+|figures-viz-pred-bin_bf| |figures-viz-pred-bin_cr|
 
-   .. figure:: ../assets/calibration/tutorial_bsd/cmap_bf_binary.png
-      :width: 50%
-      :align: center
-      :alt: Predicted data with the binary breakup and coalescence colored by Bf against the binary target data
+.. |figures-viz-pred-bin_bf| image:: ../assets/calibration/tutorial_bsd/cmap_bf_binary.png
+   :width: 49.5%
+   :alt: Predicted data with the binary breakup and coalescence colored by Bf against the binary target data
 
-   .. figure:: ../assets/calibration/tutorial_bsd/cmap_cr_binary.png
-      :width: 50%
-      :align: center
-      :alt: Predicted data with the binary breakup and coalescence colored by Cr against the binary target data
+.. |figures-viz-pred-bin_cr| image:: ../assets/calibration/tutorial_bsd/cmap_cr_binary.png
+   :width: 49.5%
+   :alt: Predicted data with the binary breakup and coalescence colored by Cr against the binary target data
 
 
 Train a neural net surrogate
@@ -152,18 +147,17 @@ Calibrate against the target data obtained with ternary breakup and coalescence
    python tut_calibration.py -ter
 
 
-.. container:: figures-cal-tern
 
-   .. figure:: ../assets/calibration/tutorial_bsd/Surr_opt_ternary_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the surrogate forward model against ternary target data 
+|figures-cal-tern-prop| |figures-cal-tern-corn|
 
-   .. figure:: ../assets/calibration/tutorial_bsd/Surr_opt_ternary_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the surrogate forward model with ternary target data 
+.. |figures-cal-tern-prop| image:: ../assets/calibration/tutorial_bsd/Surr_opt_ternary_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the surrogate forward model against ternary target data 
 
+.. |figures-cal-tern-corn| image:: ../assets/calibration/tutorial_bsd/Surr_opt_ternary_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the surrogate forward model with ternary target data 
+.. container:: figures-cal-tern
 
 
 Calibrate against the target data obtained with binary breakup and coalescence 
@@ -172,17 +166,15 @@ Calibrate against the target data obtained with binary breakup and coalescence
 
    python tut_calibration.py
 
-.. container:: figures-cal-bin
+|figures-cal-bin-prop| |figures-cal-bin-corn|
 
-   .. figure:: ../assets/calibration/tutorial_bsd/Surr_opt_binary_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the surrogate forward model against binary target data 
+.. |figures-cal-bin-prop| image:: ../assets/calibration/tutorial_bsd/Surr_opt_binary_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the surrogate forward model against binary target data 
 
-   .. figure:: ../assets/calibration/tutorial_bsd/Surr_opt_binary_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the surrogate forward model with binary target data 
+.. |figures-cal-bin-corn| image:: ../assets/calibration/tutorial_bsd/Surr_opt_binary_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the surrogate forward model with binary target data 
 
 
 Clearly, the amount of missing physics vary depending on the observations and is significantly lower when calibrating against binary breakup and coalescence data.
@@ -199,17 +191,17 @@ Calibrate against the target data obtained with ternary breakup and coalescence
 
    python tut_calibration.py -ter -cal_err
 
-.. container:: figures-cal-tern-calerr
+|figures-cal-tern-calerr-prop| |figures-cal-tern-calerr-corn|
+
+.. |figures-cal-tern-calerr-prop| image:: ../assets/calibration/tutorial_bsd/Surr_cal_ternary_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the surrogate forward model against ternary target data 
+
+.. |figures-cal-tern-calerr-corn| image:: ../assets/calibration/tutorial_bsd/Surr_cal_ternary_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the surrogate forward model with ternary target data 
 
-   .. figure:: ../assets/calibration/tutorial_bsd/Surr_cal_ternary_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the surrogate forward model against ternary target data 
 
-   .. figure:: ../assets/calibration/tutorial_bsd/Surr_cal_ternary_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the surrogate forward model with ternary target data 
 
 Calibrate against the target data obtained with binary breakup and coalescence
 
@@ -218,18 +210,16 @@ Calibrate against the target data obtained with binary breakup and coalescence
 
    python tut_calibration.py -cal_err
 
-.. container:: figures-cal-bin-calerr
 
-   .. figure:: ../assets/calibration/tutorial_bsd/Surr_cal_binary_prop.png
-      :width: 50%
-      :align: center
-      :alt: Calibrated prediction with the surrogate forward model against binary target data 
+|figures-cal-bin-calerr-prop| |figures-cal-bin-calerr-corn|
 
-   .. figure:: ../assets/calibration/tutorial_bsd/Surr_cal_binary_corner.png
-      :width: 50%
-      :align: center
-      :alt: Parameter PDF obtained with the surrogate forward model with binary target data 
+.. |figures-cal-bin-calerr-prop| image:: ../assets/calibration/tutorial_bsd/Surr_cal_binary_prop.png
+   :width: 49.5%
+   :alt: Calibrated prediction with the surrogate forward model against binary target data 
 
+.. |figures-cal-bin-calerr-corn| image:: ../assets/calibration/tutorial_bsd/Surr_cal_binary_corner.png
+   :width: 49.5%
+   :alt: Parameter PDF obtained with the surrogate forward model with binary target data 
 
 
 

docs/source/tutorials.rst

@@ -10,6 +10,6 @@ Tutorials
    :maxdepth: 3
    :caption: Tutorials contents:
 
+   bubbleColumn.rst
    calibration.rst
    calibration_bsd.rst
-   bubbleColumn.rst

tutorial_cases/calibration/bsd/post_cal.py

@@ -130,7 +130,9 @@ def post_process_cal(
         label="95% Model confidence interval",
     )
     plt.plot(rangex, std2_5_real, "--", color="k", linewidth=3)
-    pretty_labels("", "", 20, title=f"Missing phys. unc. = {sigma:.2g}")
+    pretty_labels(
+        "", "", 20, title=f"Noise + missing phys. unc. = {sigma:.2g}"
+    )
     filename = ""
     filename += "Surr"
     if args.cal_err: