Commit 4b9d643a authored by Thomas Gaskin's avatar Thomas Gaskin
Browse files

Merge branch 'use-updated-abm-plot-in-SimpleFlocking' into 'master' 

Use updated ABM plot in `SimpleFlocking` model

Closes #363

See merge request !290
parents f7e4fe4d 84cc29a2

README.md

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@@ -506,7 +506,7 @@ The following table includes the most important Python dependencies: 


| Software                  | Version  | Comments                        |

| ------------------------- | -------- | ------------------------------- |

| [utopya](https://gitlab.com/utopia-project/utopya)   | >= 1.1   | The (outsourced) Utopia frontend package |

| [utopya](https://gitlab.com/utopia-project/utopya)   | >= 1.2   | The (outsourced) Utopia frontend package |

| [dantro](https://gitlab.com/utopia-project/dantro)   | >= 0.18  | Handle, transform, and visualize hierarchically organized data |

| [paramspace](https://gitlab.com/blsqr/paramspace)    | >= 2.5   | Makes parameter sweeps easy |

cmake/modules/UtopiaEnv.cmake

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@@ -89,7 +89,7 @@ if (NOT PYTHON_PACKAGE_wheel_FOUND) 
endif()



# -- utopya

set(UTOPYA_REQUIRED_VERSION 1.1.3)

set(UTOPYA_REQUIRED_VERSION 1.2.0)



if(NOT UTOPYA_FROM_PYPI)

    set(UTOPYA_FROM_PYPI On)

doc/_cfg/SEIRD/multiverse_plots/eval.yml

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@@ -63,10 +63,8 @@ errorbars: 
    - .std: [!dag_tag infected, [seed]]

      tag: infected_std



    - operation: xr.Dataset

      kwargs:

        data_vars:

          avg: !dag_tag infected_mean

    - xr.Dataset:

      - avg: !dag_tag infected_mean

        err: !dag_tag infected_std

      tag: data  # Don't forget to define the 'data' tag
@@ -182,8 +180,7 @@ stacked_errorbands: 
        dim: seed

      tag: std

    - xr.Dataset:

        data_vars:

          infected density: !dag_tag mean

      - infected density: !dag_tag mean

        err: !dag_tag std

      tag: data
@@ -231,8 +228,7 @@ panel_errorbands: 
    - .std: [!dag_tag infected, seed]

      tag: std

    - xr.Dataset:

        data_vars:

          infected density: !dag_tag mean

      - infected density: !dag_tag mean

        err: !dag_tag std

      tag: data
@@ -274,6 +270,7 @@ panel_all: 
  color: ~

  style:

    axes.prop_cycle: cycler('color', ['#CC3333', '#006666', '#AFD8BC' ])

    savefig.transparent: true

  helpers:

    set_limits:

      y: [ 0, 0.6 ]
@@ -361,8 +358,7 @@ scatter_2d_facet: 
      tag: infected



    - xr.Dataset:

        data_vars:

          susceptible: !dag_tag susceptible

      - susceptible: !dag_tag susceptible

        infected: !dag_tag infected

      tag: data
@@ -409,8 +405,7 @@ scatter_3d: 
      tag: recovered



    - xr.Dataset:

        data_vars:

          susceptible: !dag_tag susceptible

      - susceptible: !dag_tag susceptible

        infected: !dag_tag infected

        recovered: !dag_tag infected

      tag: data

doc/_cfg/SEIRD/universe_plots/eval.yml

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@@ -48,8 +48,7 @@ _default_style: &default_style 


  transform:

    - xr.Dataset:

        data_vars:

          susceptible: !dag_tag susceptible

      - susceptible: !dag_tag susceptible

      tag: data



  dag_visualization:
@@ -111,8 +110,7 @@ debug_DAG_locate_with_vis: 
      tag: recovered



    - xr.Dataset:

        data_vars:

          susceptible: !dag_tag susceptible

      - susceptible: !dag_tag susceptible

        exposed: !dag_tag exposed

        infected: !dag_tag infected

        recovered: !dag_tag recovered
@@ -179,8 +177,7 @@ debug_DAG_advanced_print_examples: 
### END --- debug_DAG_advanced_print_examples

    # To make the plot work, just combine them here

    - xr.Dataset:

        data_vars:

          susceptible: !dag_prev

      - susceptible: !dag_prev

        exposed: !dag_prev

      tag: data
@@ -333,8 +330,7 @@ scatter_2d_simple: 
      tag: recovered



    - xr.Dataset:

        data_vars:

          susceptible: !dag_tag susceptible

      - susceptible: !dag_tag susceptible

        infected: !dag_tag infected

        recovered: !dag_tag recovered

      tag: data
@@ -372,8 +368,7 @@ scatter_2d: 
      kwargs: { drop: true }

      tag: recovered

    - xr.Dataset:

        data_vars:

          susceptible: !dag_tag susceptible

      - susceptible: !dag_tag susceptible

        infected: !dag_tag infected

        recovered: !dag_tag recovered

      tag: data
@@ -415,10 +410,8 @@ scatter_3d: 
    - .sel: [!dag_tag kind, { kind: recovered }]

      kwargs: { drop: true }

      tag: recovered

    - operation: xr.Dataset

      kwargs:

        data_vars:

          susceptible: !dag_tag susceptible

    - xr.Dataset:

      - susceptible: !dag_tag susceptible

        infected: !dag_tag infected

        recovered: !dag_tag recovered

      tag: data

doc/_cfg/SimpleFlocking/demo/eval.yml

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# Output for the demo scenario

---



_utopia_colors: &utopia_colors

  dark_blue:          &darkblue           '#003366'

  medium_blue:        &mediumblue         '#0099CC'

  light_blue:         &lightblue          '#99CCFF'

  dark_green:         &darkgreen          '#006666'

  medium_green:       &mediumgreen        '#339999'

  light_green:        &lightgreen         '#AFD8BC'

  yellow:             &yellow             '#FFCC66'

  red:                &red                '#CC3333'

  cream_white:        &creamwhite         '#F6F6F6'

  white:              &white              '#fff'

  black:              &black              '#000000'

  gray:               &gray               '#F7F9FF'

  dark_gray:          &darkgray           '#666666'





# -----------------------------------------------------------------------------



# Demonstrates agents in a domain

### Start --- agents_in_domain

agents:



  based_on:

    - .creator.universe

    - .plot.abm

    - .animation.ffmpeg

    - .animation.fps30



  # Prepare data

  select:

    x:

      path: agent/x

      transform: [ .data ]

      allow_failure: silent

      fallback: !dag_tag _skip_plot

    y:

      path: agent/y

      transform: [ .data ]

    orientation:

      path: agent/orientation

      transform: [ .data ]



    space_extent:

      path: agent/x  # meta data is written to every other dataset as well

      transform:

        - getattr: [ !dag_prev , attrs ]

        - getitem: [ !dag_prev , space_extent ]



  transform:

    # Combine data into one dataset

    - xr.Dataset:

        - x: !dag_tag x

          y: !dag_tag y

          orientation: !dag_tag orientation

      tag: agents



  # Data encoding

  x: x

  y: y

  frames: time

  orientation: orientation

  hue: orientation



  # Define what to plot

  to_plot:

    agents:

      marker: wedge



  # Pass on space extent (used for setting limits)

  domain:

    extent: !dag_result space_extent

    pad: 0



  # Set tail lengths, style, and decay factor

  tail_length: 24

  tail_decay: 0.12

  tail_max_segment_length: 1.  # to avoid problems when crossing a boundary

  tail_kwargs:

    color: black

    linewidth: 0.5

    alpha: .6

    zorder: -10



  # Colorbar settings

  vmin: -3.14159

  vmax: +3.14159

  cbar_labels:

    +3.14159: $+π$

    +1.570795: $+π/2$

    0: $0$

    -1.570795: $+π/2$

    -3.14159: $-π$



### End --- agents_in_domain

  enabled: true



  universes:

    seed: [ 0 ]

  # Use a Utopia-themed colormap

  cmap: &cmap

    continuous: true

    from_values:

      0.0: *darkgreen

      0.333: *yellow

      0.666: *red

      1.0: *darkgreen

  frames_isel: !range [ 200 ]





fish_demo:

  based_on:

    - agents

    - .animation.disabled

  frames_isel: [10]

  to_plot:

    agents:

      marker: fish2



agents_in_domain_clean:

  based_on:

    - agents_in_domain

    - .animation.fps30

    - .animation.very_high_dpi

    # - .animation.frames



    # Hide axes

    - .hlpr.ticks.x.hide

    - .hlpr.ticks.y.hide

    - .style.no_spines

    - .style.no_grid



  figsize_aspect_offset: 0

  suptitle_fstr: false

  add_colorbar: false

  add_legend: false



  style:

    axes.facecolor: *gray



  cmap:

    <<: *cmap



  universes:

    seed: [ 1, 2 ]



agents_in_domain_clean_frames:

  enabled: false

  based_on:

    - agents_in_domain_clean

    - .animation.frames



  marker: fish