From 72e1686c0166adab88bdd7567714d36984266649 Mon Sep 17 00:00:00 2001 From: Yin-Chi Chan Date: Sun, 5 May 2024 06:54:50 +0100 Subject: [PATCH] Documentation --- docs/conf.py | 8 + docs/html/.buildinfo | 2 +- docs/html/_modules/histopath_bim_des/bim.html | 15 +- .../histopath_bim_des/config/arrivals.html | 15 +- .../histopath_bim_des/config/batching.html | 15 +- .../histopath_bim_des/config/config.html | 15 +- .../config/distributions.html | 15 +- .../histopath_bim_des/config/global_vars.html | 15 +- .../histopath_bim_des/config/resources.html | 15 +- .../histopath_bim_des/config/runners.html | 15 +- .../histopath_bim_des/config/tasks.html | 15 +- .../histopath_bim_des/distribution.html | 15 +- .../_modules/histopath_bim_des/excel.html | 15 +- .../_modules/histopath_bim_des/model.html | 15 +- .../histopath_bim_des/process/core.html | 15 +- .../process/p10_reception.html | 15 +- .../histopath_bim_des/process/p20_cutup.html | 15 +- .../process/p30_processing.html | 15 +- .../process/p40_microtomy.html | 15 +- .../process/p50_staining.html | 15 +- .../process/p60_labelling.html | 15 +- .../process/p70_scanning.html | 15 +- .../histopath_bim_des/process/p80_qc.html | 15 +- .../process/p90_reporting.html | 15 +- .../_modules/histopath_bim_des/specimens.html | 15 +- docs/html/_modules/index.html | 15 +- docs/html/_sources/index.rst.txt | 34 ++-- docs/html/_sources/installation.md.txt | 33 ++++ docs/html/_sources/thirdparty.md.txt | 28 ++++ docs/html/apidoc/histopath_bim_des.bim.html | 17 +- .../histopath_bim_des.config.arrivals.html | 17 +- .../histopath_bim_des.config.batching.html | 17 +- .../histopath_bim_des.config.config.html | 17 +- ...istopath_bim_des.config.distributions.html | 17 +- .../histopath_bim_des.config.global_vars.html | 17 +- .../html/apidoc/histopath_bim_des.config.html | 17 +- .../histopath_bim_des.config.resources.html | 17 +- .../histopath_bim_des.config.runners.html | 17 +- .../histopath_bim_des.config.tasks.html | 17 +- .../histopath_bim_des.distribution.html | 17 +- docs/html/apidoc/histopath_bim_des.excel.html | 17 +- docs/html/apidoc/histopath_bim_des.html | 21 ++- docs/html/apidoc/histopath_bim_des.model.html | 17 +- .../histopath_bim_des.process.core.html | 17 +- .../apidoc/histopath_bim_des.process.html | 17 +- ...stopath_bim_des.process.p10_reception.html | 17 +- .../histopath_bim_des.process.p20_cutup.html | 17 +- ...topath_bim_des.process.p30_processing.html | 17 +- ...stopath_bim_des.process.p40_microtomy.html | 17 +- ...istopath_bim_des.process.p50_staining.html | 17 +- ...stopath_bim_des.process.p60_labelling.html | 17 +- ...istopath_bim_des.process.p70_scanning.html | 17 +- .../histopath_bim_des.process.p80_qc.html | 17 +- ...stopath_bim_des.process.p90_reporting.html | 17 +- .../apidoc/histopath_bim_des.specimens.html | 17 +- docs/html/apidoc/histopath_bim_des.util.html | 17 +- docs/html/apidoc/modules.html | 17 +- docs/html/config.html | 17 +- docs/html/genindex.html | 16 +- docs/html/index.html | 55 +++--- docs/html/installation.html | 157 ++++++++++++++++++ docs/html/objects.inv | Bin 4137 -> 4177 bytes docs/html/processes.html | 21 ++- docs/html/py-modindex.html | 15 +- docs/html/search.html | 15 +- docs/html/searchindex.js | 2 +- docs/html/simulation.html | 17 +- docs/html/thirdparty.html | 153 +++++++++++++++++ docs/index.rst | 34 ++-- docs/installation.md | 33 ++++ docs/thirdparty.md | 28 ++++ 71 files changed, 1302 insertions(+), 206 deletions(-) create mode 100644 docs/html/_sources/installation.md.txt create mode 100644 docs/html/_sources/thirdparty.md.txt create mode 100644 docs/html/installation.html create mode 100644 docs/html/thirdparty.html create mode 100644 docs/installation.md create mode 100644 docs/thirdparty.md diff --git a/docs/conf.py b/docs/conf.py index 41e1372..f630f58 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -51,3 +51,11 @@ html_theme = 'sphinx_rtd_theme' html_static_path = ['_static'] + +html_context = { + 'display_github': True, + 'github_user': 'yinchi', + 'github_repo': 'histopath-bim-des', + 'github_version': 'main', + 'conf_py_path': '/docs/', +} diff --git a/docs/html/.buildinfo b/docs/html/.buildinfo index 5d1ce61..1caad31 100644 --- a/docs/html/.buildinfo +++ b/docs/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 661ee7406388d085c75b2b522d567f0f +config: 45d9ac09b073bccebfd8d6a9241ca14a tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/html/_modules/histopath_bim_des/bim.html b/docs/html/_modules/histopath_bim_des/bim.html index 5ace3d1..087d933 100644 --- a/docs/html/_modules/histopath_bim_des/bim.html +++ b/docs/html/_modules/histopath_bim_des/bim.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/config/arrivals.html b/docs/html/_modules/histopath_bim_des/config/arrivals.html index 01e0f0b..a3cefd5 100644 --- a/docs/html/_modules/histopath_bim_des/config/arrivals.html +++ b/docs/html/_modules/histopath_bim_des/config/arrivals.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/config/batching.html b/docs/html/_modules/histopath_bim_des/config/batching.html index 19436e0..68c354e 100644 --- a/docs/html/_modules/histopath_bim_des/config/batching.html +++ b/docs/html/_modules/histopath_bim_des/config/batching.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/config/config.html b/docs/html/_modules/histopath_bim_des/config/config.html index f04e3ed..d820f78 100644 --- a/docs/html/_modules/histopath_bim_des/config/config.html +++ b/docs/html/_modules/histopath_bim_des/config/config.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/config/distributions.html b/docs/html/_modules/histopath_bim_des/config/distributions.html index e6d0571..451114a 100644 --- a/docs/html/_modules/histopath_bim_des/config/distributions.html +++ b/docs/html/_modules/histopath_bim_des/config/distributions.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/config/global_vars.html b/docs/html/_modules/histopath_bim_des/config/global_vars.html index 532358c..52b4890 100644 --- a/docs/html/_modules/histopath_bim_des/config/global_vars.html +++ b/docs/html/_modules/histopath_bim_des/config/global_vars.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/config/resources.html b/docs/html/_modules/histopath_bim_des/config/resources.html index 1af758a..8ca8228 100644 --- a/docs/html/_modules/histopath_bim_des/config/resources.html +++ b/docs/html/_modules/histopath_bim_des/config/resources.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/config/runners.html b/docs/html/_modules/histopath_bim_des/config/runners.html index 218930b..dd0fb7f 100644 --- a/docs/html/_modules/histopath_bim_des/config/runners.html +++ b/docs/html/_modules/histopath_bim_des/config/runners.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/config/tasks.html b/docs/html/_modules/histopath_bim_des/config/tasks.html index 0f8053a..cc51170 100644 --- a/docs/html/_modules/histopath_bim_des/config/tasks.html +++ b/docs/html/_modules/histopath_bim_des/config/tasks.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/distribution.html b/docs/html/_modules/histopath_bim_des/distribution.html index 98c9a3b..cad54ac 100644 --- a/docs/html/_modules/histopath_bim_des/distribution.html +++ b/docs/html/_modules/histopath_bim_des/distribution.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/excel.html b/docs/html/_modules/histopath_bim_des/excel.html index 16fa6cd..13a3a4d 100644 --- a/docs/html/_modules/histopath_bim_des/excel.html +++ b/docs/html/_modules/histopath_bim_des/excel.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/model.html b/docs/html/_modules/histopath_bim_des/model.html index 32316ad..c609618 100644 --- a/docs/html/_modules/histopath_bim_des/model.html +++ b/docs/html/_modules/histopath_bim_des/model.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/core.html b/docs/html/_modules/histopath_bim_des/process/core.html index 29e1062..fd11233 100644 --- a/docs/html/_modules/histopath_bim_des/process/core.html +++ b/docs/html/_modules/histopath_bim_des/process/core.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/p10_reception.html b/docs/html/_modules/histopath_bim_des/process/p10_reception.html index 79764c1..ec6d2c9 100644 --- a/docs/html/_modules/histopath_bim_des/process/p10_reception.html +++ b/docs/html/_modules/histopath_bim_des/process/p10_reception.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/p20_cutup.html b/docs/html/_modules/histopath_bim_des/process/p20_cutup.html index 9753861..057bb70 100644 --- a/docs/html/_modules/histopath_bim_des/process/p20_cutup.html +++ b/docs/html/_modules/histopath_bim_des/process/p20_cutup.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/p30_processing.html b/docs/html/_modules/histopath_bim_des/process/p30_processing.html index b375b8b..3a86680 100644 --- a/docs/html/_modules/histopath_bim_des/process/p30_processing.html +++ b/docs/html/_modules/histopath_bim_des/process/p30_processing.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/p40_microtomy.html b/docs/html/_modules/histopath_bim_des/process/p40_microtomy.html index 430ff2f..86274a4 100644 --- a/docs/html/_modules/histopath_bim_des/process/p40_microtomy.html +++ b/docs/html/_modules/histopath_bim_des/process/p40_microtomy.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/p50_staining.html b/docs/html/_modules/histopath_bim_des/process/p50_staining.html index 00b7ca6..44da3af 100644 --- a/docs/html/_modules/histopath_bim_des/process/p50_staining.html +++ b/docs/html/_modules/histopath_bim_des/process/p50_staining.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/p60_labelling.html b/docs/html/_modules/histopath_bim_des/process/p60_labelling.html index 3e04579..d0191b6 100644 --- a/docs/html/_modules/histopath_bim_des/process/p60_labelling.html +++ b/docs/html/_modules/histopath_bim_des/process/p60_labelling.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/p70_scanning.html b/docs/html/_modules/histopath_bim_des/process/p70_scanning.html index 2c7ee1f..d33f6e1 100644 --- a/docs/html/_modules/histopath_bim_des/process/p70_scanning.html +++ b/docs/html/_modules/histopath_bim_des/process/p70_scanning.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/p80_qc.html b/docs/html/_modules/histopath_bim_des/process/p80_qc.html index c0334b7..7e83c14 100644 --- a/docs/html/_modules/histopath_bim_des/process/p80_qc.html +++ b/docs/html/_modules/histopath_bim_des/process/p80_qc.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/process/p90_reporting.html b/docs/html/_modules/histopath_bim_des/process/p90_reporting.html index b0f537f..6c626cb 100644 --- a/docs/html/_modules/histopath_bim_des/process/p90_reporting.html +++ b/docs/html/_modules/histopath_bim_des/process/p90_reporting.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/histopath_bim_des/specimens.html b/docs/html/_modules/histopath_bim_des/specimens.html index 13e3542..684794e 100644 --- a/docs/html/_modules/histopath_bim_des/specimens.html +++ b/docs/html/_modules/histopath_bim_des/specimens.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_modules/index.html b/docs/html/_modules/index.html index 68df053..93b3ae0 100644 --- a/docs/html/_modules/index.html +++ b/docs/html/_modules/index.html @@ -43,14 +43,25 @@ diff --git a/docs/html/_sources/index.rst.txt b/docs/html/_sources/index.rst.txt index 738517a..6d8f5d7 100644 --- a/docs/html/_sources/index.rst.txt +++ b/docs/html/_sources/index.rst.txt @@ -3,8 +3,9 @@ BIM-DES integration demo **Authors:** -* Yin-Chi Chan, Institute for Manufacturing, University of Cambridge (maintainer) -* Nicola Moretti, Bartlett School of Sustainable Construction, University College London +* `Yin-Chi Chan `_, + Institute for Manufacturing, University of Cambridge (maintainer) +* `Nicola Moretti `_, Bartlett School of Sustainable Construction, University College London This Python package contains code for a BIM-DES (building information modelling and discrete event simulation) integration model of the histopathology lab at Addenbrooke's Hospital, Cambridge, UK. @@ -16,26 +17,39 @@ as the proportion of specimens completed within a given number of days. By enabling or disabling pathways in the parsed .ifc file, different runner times will be calculated, resulting in different performance with respect to the key performance indicators (KPIs) such as mean lab turnaround time (TAT) and service level (% of lab TAT less than *N* days). -Examples can be found in the ``notebooks/`` directory of this project. +Examples can be found in the `notebooks/ `_ directory of this project. + .. toctree:: :maxdepth: 2 :caption: Contents + :hidden: + Jupyter notebooks πŸ”— config simulation processes - Jupyter notebooks .. toctree:: :maxdepth: 2 - :caption: API reference: + :caption: Technical + :hidden: + + Installation ⬇️ + Third-party libraries πŸ“š + +.. toctree:: + :maxdepth: 2 + :caption: API reference πŸ“– + :hidden: apidoc/histopath_bim_des -Indices and tables -================== +.. toctree:: + :maxdepth: 0 + :caption: Indicies and Tables πŸ” + :hidden: -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` + genindex + modindex + search diff --git a/docs/html/_sources/installation.md.txt b/docs/html/_sources/installation.md.txt new file mode 100644 index 0000000..1627dda --- /dev/null +++ b/docs/html/_sources/installation.md.txt @@ -0,0 +1,33 @@ +# Installation + +This project was developed using the [Poetry](https://python-poetry.org/) package manager and +Python 3.12. To install the Python package and its dependencies, the following bash scripts can +be used: + +```bash +pip install poetry +``` +**OR** +```bash +sudo apt-get install python3-poetry +``` + +The second form is necessary if the pip option returns an +"`This environment is externally managed`" error. + +```bash +git clone https://github.com/yinchi/histopath-bim-des +cd histopath-bim-des + +# if you have obtained a copy of histo.ifc +mkdir -p assets/private/ +cp /path/to/histo.ifc assets/private/ + +# required by erdantic +sudo apt install libgraphviz-dev + +# If 3.12 is not the default Python version +poetry venv use /usr/bin/python3/12 + +poetry install +``` diff --git a/docs/html/_sources/thirdparty.md.txt b/docs/html/_sources/thirdparty.md.txt new file mode 100644 index 0000000..395b35a --- /dev/null +++ b/docs/html/_sources/thirdparty.md.txt @@ -0,0 +1,28 @@ +# Third-party libraries + +This project depends on a number of third-party Python libraries: + +**General:** + +* [poetry](https://python-poetry.org/): package manager +* [salabim](https://www.salabim.org/): discrete-event simulation + +**BIM integration:** + +* [ifcopenshell](https://ifcopenshell.org/): Industry Foundation Classes +* [networkx](https://networkx.org/): graph/network analysis +* [shapely](https://shapely.readthedocs.io/): geometric analysis + + +**Data analysis:** + +* [openpyxl](https://openpyxl.readthedocs.io/): Excel file API +* [pandas](https://pandas.pydata.org/): dataframes +* [scipy](https://scipy.org/): scientific computing (statistics, optimisation, linear algebra...) + +**Data representation and validation:** + +* [pydantic](https://docs.pydantic.dev/): dataclasses with validation +* [dacite](https://github.com/konradhalas/dacite/): construct Python dataclasses from dicts + +For a full list of libraries, see the project's `pyproject.toml` file. diff --git a/docs/html/apidoc/histopath_bim_des.bim.html b/docs/html/apidoc/histopath_bim_des.bim.html index 7daa771..6263de7 100644 --- a/docs/html/apidoc/histopath_bim_des.bim.html +++ b/docs/html/apidoc/histopath_bim_des.bim.html @@ -46,12 +46,17 @@ @@ -92,7 +103,7 @@
  • histopath_bim_des package
  • histopath_bim_des.bim module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.config.arrivals.html b/docs/html/apidoc/histopath_bim_des.config.arrivals.html index 7851f61..5964bb3 100644 --- a/docs/html/apidoc/histopath_bim_des.config.arrivals.html +++ b/docs/html/apidoc/histopath_bim_des.config.arrivals.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.config package
  • histopath_bim_des.config.arrivals module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.config.batching.html b/docs/html/apidoc/histopath_bim_des.config.batching.html index e73670d..1029c72 100644 --- a/docs/html/apidoc/histopath_bim_des.config.batching.html +++ b/docs/html/apidoc/histopath_bim_des.config.batching.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.config package
  • histopath_bim_des.config.batching module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.config.config.html b/docs/html/apidoc/histopath_bim_des.config.config.html index 49edc2e..e0c43c8 100644 --- a/docs/html/apidoc/histopath_bim_des.config.config.html +++ b/docs/html/apidoc/histopath_bim_des.config.config.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.config package
  • histopath_bim_des.config.config module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.config.distributions.html b/docs/html/apidoc/histopath_bim_des.config.distributions.html index 173dfa3..08442f3 100644 --- a/docs/html/apidoc/histopath_bim_des.config.distributions.html +++ b/docs/html/apidoc/histopath_bim_des.config.distributions.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.config package
  • histopath_bim_des.config.distributions module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.config.global_vars.html b/docs/html/apidoc/histopath_bim_des.config.global_vars.html index b82ff7b..2df9028 100644 --- a/docs/html/apidoc/histopath_bim_des.config.global_vars.html +++ b/docs/html/apidoc/histopath_bim_des.config.global_vars.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.config package
  • histopath_bim_des.config.global_vars module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.config.html b/docs/html/apidoc/histopath_bim_des.config.html index 2c98432..d6f424b 100644 --- a/docs/html/apidoc/histopath_bim_des.config.html +++ b/docs/html/apidoc/histopath_bim_des.config.html @@ -46,12 +46,17 @@ @@ -86,7 +97,7 @@
  • histopath_bim_des package
  • histopath_bim_des.config package
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.config.resources.html b/docs/html/apidoc/histopath_bim_des.config.resources.html index c4cb4bb..36e360d 100644 --- a/docs/html/apidoc/histopath_bim_des.config.resources.html +++ b/docs/html/apidoc/histopath_bim_des.config.resources.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.config package
  • histopath_bim_des.config.resources module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.config.runners.html b/docs/html/apidoc/histopath_bim_des.config.runners.html index c0b64d7..15a3b33 100644 --- a/docs/html/apidoc/histopath_bim_des.config.runners.html +++ b/docs/html/apidoc/histopath_bim_des.config.runners.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.config package
  • histopath_bim_des.config.runners module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.config.tasks.html b/docs/html/apidoc/histopath_bim_des.config.tasks.html index 4be3123..808ab0b 100644 --- a/docs/html/apidoc/histopath_bim_des.config.tasks.html +++ b/docs/html/apidoc/histopath_bim_des.config.tasks.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.config package
  • histopath_bim_des.config.tasks module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.distribution.html b/docs/html/apidoc/histopath_bim_des.distribution.html index 9d7e13f..9d30b25 100644 --- a/docs/html/apidoc/histopath_bim_des.distribution.html +++ b/docs/html/apidoc/histopath_bim_des.distribution.html @@ -46,12 +46,17 @@ @@ -96,7 +107,7 @@
  • histopath_bim_des package
  • histopath_bim_des.distribution module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.excel.html b/docs/html/apidoc/histopath_bim_des.excel.html index 13f79f9..4f3368c 100644 --- a/docs/html/apidoc/histopath_bim_des.excel.html +++ b/docs/html/apidoc/histopath_bim_des.excel.html @@ -46,12 +46,17 @@ @@ -92,7 +103,7 @@
  • histopath_bim_des package
  • histopath_bim_des.excel module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.html b/docs/html/apidoc/histopath_bim_des.html index 6c8b457..3e37f4d 100644 --- a/docs/html/apidoc/histopath_bim_des.html +++ b/docs/html/apidoc/histopath_bim_des.html @@ -22,7 +22,7 @@ - + @@ -46,12 +46,17 @@ @@ -89,7 +100,7 @@
  • histopath_bim_des package
  • - View page source + Edit on GitHub
    • @@ -507,7 +518,7 @@

    Submodules - + diff --git a/docs/html/apidoc/histopath_bim_des.model.html b/docs/html/apidoc/histopath_bim_des.model.html index 2b18aac..7a63bf1 100644 --- a/docs/html/apidoc/histopath_bim_des.model.html +++ b/docs/html/apidoc/histopath_bim_des.model.html @@ -46,12 +46,17 @@ @@ -94,7 +105,7 @@
  • histopath_bim_des package
  • histopath_bim_des.model module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.core.html b/docs/html/apidoc/histopath_bim_des.process.core.html index 901595b..2734ac4 100644 --- a/docs/html/apidoc/histopath_bim_des.process.core.html +++ b/docs/html/apidoc/histopath_bim_des.process.core.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.core module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.html b/docs/html/apidoc/histopath_bim_des.process.html index fdd820e..19369f7 100644 --- a/docs/html/apidoc/histopath_bim_des.process.html +++ b/docs/html/apidoc/histopath_bim_des.process.html @@ -46,12 +46,17 @@ @@ -86,7 +97,7 @@
  • histopath_bim_des package
  • histopath_bim_des.process package
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.p10_reception.html b/docs/html/apidoc/histopath_bim_des.process.p10_reception.html index ea34a67..07f5718 100644 --- a/docs/html/apidoc/histopath_bim_des.process.p10_reception.html +++ b/docs/html/apidoc/histopath_bim_des.process.p10_reception.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.p10_reception module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.p20_cutup.html b/docs/html/apidoc/histopath_bim_des.process.p20_cutup.html index 86a754e..b0c6e59 100644 --- a/docs/html/apidoc/histopath_bim_des.process.p20_cutup.html +++ b/docs/html/apidoc/histopath_bim_des.process.p20_cutup.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.p20_cutup module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.p30_processing.html b/docs/html/apidoc/histopath_bim_des.process.p30_processing.html index 61c0ba1..850deb3 100644 --- a/docs/html/apidoc/histopath_bim_des.process.p30_processing.html +++ b/docs/html/apidoc/histopath_bim_des.process.p30_processing.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.p30_processing module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.p40_microtomy.html b/docs/html/apidoc/histopath_bim_des.process.p40_microtomy.html index 392aafc..6ce44f2 100644 --- a/docs/html/apidoc/histopath_bim_des.process.p40_microtomy.html +++ b/docs/html/apidoc/histopath_bim_des.process.p40_microtomy.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.p40_microtomy module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.p50_staining.html b/docs/html/apidoc/histopath_bim_des.process.p50_staining.html index c9003cc..0020d73 100644 --- a/docs/html/apidoc/histopath_bim_des.process.p50_staining.html +++ b/docs/html/apidoc/histopath_bim_des.process.p50_staining.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.p50_staining module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.p60_labelling.html b/docs/html/apidoc/histopath_bim_des.process.p60_labelling.html index ba5abba..49489d8 100644 --- a/docs/html/apidoc/histopath_bim_des.process.p60_labelling.html +++ b/docs/html/apidoc/histopath_bim_des.process.p60_labelling.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.p60_labelling module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.p70_scanning.html b/docs/html/apidoc/histopath_bim_des.process.p70_scanning.html index 24958e5..e7ca1d3 100644 --- a/docs/html/apidoc/histopath_bim_des.process.p70_scanning.html +++ b/docs/html/apidoc/histopath_bim_des.process.p70_scanning.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.p70_scanning module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.p80_qc.html b/docs/html/apidoc/histopath_bim_des.process.p80_qc.html index 4c4713a..a1fb28e 100644 --- a/docs/html/apidoc/histopath_bim_des.process.p80_qc.html +++ b/docs/html/apidoc/histopath_bim_des.process.p80_qc.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.p80_qc module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.process.p90_reporting.html b/docs/html/apidoc/histopath_bim_des.process.p90_reporting.html index bf1cc81..124b9b7 100644 --- a/docs/html/apidoc/histopath_bim_des.process.p90_reporting.html +++ b/docs/html/apidoc/histopath_bim_des.process.p90_reporting.html @@ -46,12 +46,17 @@ @@ -87,7 +98,7 @@
  • histopath_bim_des.process package
  • histopath_bim_des.process.p90_reporting module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.specimens.html b/docs/html/apidoc/histopath_bim_des.specimens.html index c81302b..a95f42f 100644 --- a/docs/html/apidoc/histopath_bim_des.specimens.html +++ b/docs/html/apidoc/histopath_bim_des.specimens.html @@ -46,12 +46,17 @@ @@ -94,7 +105,7 @@
  • histopath_bim_des package
  • histopath_bim_des.specimens module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/histopath_bim_des.util.html b/docs/html/apidoc/histopath_bim_des.util.html index 213d75a..8632c28 100644 --- a/docs/html/apidoc/histopath_bim_des.util.html +++ b/docs/html/apidoc/histopath_bim_des.util.html @@ -45,12 +45,17 @@ @@ -89,7 +100,7 @@
  • histopath_bim_des package
  • histopath_bim_des.util module
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/apidoc/modules.html b/docs/html/apidoc/modules.html index 1fd276d..2fcd512 100644 --- a/docs/html/apidoc/modules.html +++ b/docs/html/apidoc/modules.html @@ -44,14 +44,25 @@ @@ -70,7 +81,7 @@
  • histopath_bim_des
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/config.html b/docs/html/config.html index 8f8e82d..5894a3a 100644 --- a/docs/html/config.html +++ b/docs/html/config.html @@ -46,17 +46,28 @@ @@ -75,7 +86,7 @@
  • Model Configuration
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/genindex.html b/docs/html/genindex.html index befd5ac..484325e 100644 --- a/docs/html/genindex.html +++ b/docs/html/genindex.html @@ -43,14 +43,25 @@ @@ -69,6 +80,7 @@
  • Index
  • + Edit on GitHub
    • diff --git a/docs/html/index.html b/docs/html/index.html index 86623d1..166f0ae 100644 --- a/docs/html/index.html +++ b/docs/html/index.html @@ -45,14 +45,25 @@ @@ -71,7 +82,7 @@
  • BIM-DES integration demo
  • - View page source + Edit on GitHub
    • @@ -83,8 +94,9 @@

    BIM-DES integration demo

    Authors:

      -

    • Yin-Chi Chan, Institute for Manufacturing, University of Cambridge (maintainer)

      • -

    • Nicola Moretti, Bartlett School of Sustainable Construction, University College London

      • +

    • Yin-Chi Chan, +Institute for Manufacturing, University of Cambridge (maintainer)

      • +

    • Nicola Moretti, Bartlett School of Sustainable Construction, University College London

    This Python package contains code for a BIM-DES (building information modelling and discrete event simulation) integration model of the histopathology lab at Addenbrooke’s Hospital, Cambridge, UK. @@ -95,38 +107,15 @@

    BIM-DES integration demonotebooks/ directory of this project.

    +Examples can be found in the     notebooks/ directory of this project.

    +
    +
    +
    +
    -

    Contents

    -
    -

    API reference:

    -
    - -
    -

    Indices and tables

    -
    diff --git a/docs/html/installation.html b/docs/html/installation.html new file mode 100644 index 0000000..c4742c6 --- /dev/null +++ b/docs/html/installation.html @@ -0,0 +1,157 @@ + + + + + + + Installation — histopath-bim-des 0.0.0 documentation + + + + + + + + + + + + + + + + + + + +
    + + +
    + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    Installation

    +

    This project was developed using the Poetry package manager and +Python 3.12. To install the Python package and its dependencies, the following bash scripts can +be used:

    +
    pip install poetry
+
    +
    +

    OR

    +
    sudo apt-get install python3-poetry
+
    +
    +

    The second form is necessary if the pip option returns an +β€œThis environment is externally managed” error.

    +
    git clone https://github.com/yinchi/histopath-bim-des
+cd histopath-bim-des
+
+# if you have obtained a copy of histo.ifc
+mkdir -p assets/private/
+cp /path/to/histo.ifc assets/private/
+
+# required by erdantic
+sudo apt install libgraphviz-dev
+
+# If 3.12 is not the default Python version
+poetry venv use /usr/bin/python3/12
+
+poetry install
+
    +
    +
    + + +
    +
    + +
    +
    +
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  • Histopathology processes
  • - View page source + Edit on GitHub
    • @@ -93,7 +104,7 @@

    Histopathology processes - +
    diff --git a/docs/html/py-modindex.html b/docs/html/py-modindex.html index 3c0c652..e60df7c 100644 --- a/docs/html/py-modindex.html +++ b/docs/html/py-modindex.html @@ -46,14 +46,25 @@ diff --git a/docs/html/search.html b/docs/html/search.html index 191fede..f2b532f 100644 --- a/docs/html/search.html +++ b/docs/html/search.html @@ -46,14 +46,25 @@ diff --git a/docs/html/searchindex.js b/docs/html/searchindex.js index 73e03ea..63e5d06 100644 --- a/docs/html/searchindex.js +++ b/docs/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"API reference:": [[29, null]], "BIM-DES integration demo": [[29, "bim-des-integration-demo"]], "Contents": [[29, null]], "Generating a runner times configuration": [[28, "generating-a-runner-times-configuration"]], "Histopathology processes": [[30, "histopathology-processes"]], "Indices and tables": [[29, "indices-and-tables"]], "Model Configuration": [[28, "model-configuration"]], "Module contents": [[0, "module-histopath_bim_des"], [2, 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(histopath_bim_des.specimens.priority attribute)": [[25, "histopath_bim_des.specimens.Priority.PRIORITY", false]], "prob_bms_cutup (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_bms_cutup", false]], "prob_bms_cutup (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_bms_cutup", false]], "prob_bms_cutup_urgent (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_bms_cutup_urgent", false]], "prob_bms_cutup_urgent (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_bms_cutup_urgent", false]], "prob_decalc_bone (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_decalc_bone", false]], "prob_decalc_bone (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_decalc_bone", false]], "prob_decalc_oven (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_decalc_oven", false]], "prob_decalc_oven (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_decalc_oven", false]], "prob_internal (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_internal", false]], "prob_internal (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_internal", false]], "prob_invest_easy (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_invest_easy", false]], "prob_invest_easy (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_invest_easy", false]], "prob_invest_external (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_invest_external", false]], "prob_invest_external (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_invest_external", false]], "prob_invest_hard (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_invest_hard", false]], "prob_invest_hard (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_invest_hard", false]], "prob_large_cutup (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_large_cutup", false]], "prob_large_cutup (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_large_cutup", false]], "prob_large_cutup_urgent (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_large_cutup_urgent", false]], "prob_large_cutup_urgent (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_large_cutup_urgent", false]], "prob_mega_blocks (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_mega_blocks", false]], "prob_mega_blocks (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_mega_blocks", false]], "prob_microtomy_levels (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_microtomy_levels", false]], "prob_microtomy_levels (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_microtomy_levels", false]], "prob_pool_cutup (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_pool_cutup", false]], "prob_pool_cutup (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_pool_cutup", false]], "prob_pool_cutup_urgent (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_pool_cutup_urgent", false]], "prob_pool_cutup_urgent (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_pool_cutup_urgent", false]], "prob_prebook (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_prebook", false]], "prob_prebook (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_prebook", false]], "prob_priority_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_priority_cancer", false]], "prob_priority_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_priority_cancer", false]], "prob_priority_non_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_priority_non_cancer", false]], "prob_priority_non_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_priority_non_cancer", false]], "prob_urgent_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_urgent_cancer", false]], "prob_urgent_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_urgent_cancer", false]], "prob_urgent_non_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_urgent_non_cancer", false]], "prob_urgent_non_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_urgent_non_cancer", false]], "process (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.Process", false]], "process() (histopath_bim_des.process.core.arrivalgenerator method)": [[15, "histopath_bim_des.process.core.ArrivalGenerator.process", false]], "process() (histopath_bim_des.process.core.baseprocess method)": [[15, "histopath_bim_des.process.core.BaseProcess.process", false]], "process() (histopath_bim_des.process.core.batchingprocess method)": [[15, "histopath_bim_des.process.core.BatchingProcess.process", false]], "process() (histopath_bim_des.process.core.collationprocess method)": [[15, "histopath_bim_des.process.core.CollationProcess.process", false]], "process() (histopath_bim_des.process.core.deliveryprocess method)": [[15, "histopath_bim_des.process.core.DeliveryProcess.process", false]], "process() (histopath_bim_des.process.core.process method)": [[15, "histopath_bim_des.process.core.Process.process", false]], "process() (histopath_bim_des.process.core.resourcescheduler method)": [[15, "histopath_bim_des.process.core.ResourceScheduler.process", false]], "process() (histopath_bim_des.specimens.specimen method)": [[25, "histopath_bim_des.specimens.Specimen.process", false]], "processdoormap (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap", false]], "processes (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.processes", false]], "processing (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.processing", false]], "processing_assign_queue() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_assign_queue", false]], "processing_generic() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_generic", false]], "processing_large_surgicals (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_large_surgicals", false]], "processing_large_surgicals (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_large_surgicals", false]], "processing_larges() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_larges", false]], "processing_machine (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.processing_machine", false]], "processing_machine (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.processing_machine", false]], "processing_megas (histopath_bim_des.config.batching.batchsizes attribute)": [[4, "histopath_bim_des.config.batching.BatchSizes.processing_megas", false]], "processing_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_megas", false]], "processing_megas (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_megas", false]], "processing_megas() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_megas", false]], "processing_microtomy (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.processing_microtomy", false]], "processing_microtomy (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.processing_microtomy", false]], "processing_regular (histopath_bim_des.config.batching.batchsizes attribute)": [[4, "histopath_bim_des.config.batching.BatchSizes.processing_regular", false]], "processing_room_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.processing_room_staff", false]], "processing_room_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.processing_room_staff", false]], "processing_small_surgicals (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_small_surgicals", false]], "processing_small_surgicals (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_small_surgicals", false]], "processing_smalls() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_smalls", false]], "processing_start() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_start", false]], "processing_urgent (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_urgent", false]], "processing_urgent (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_urgent", false]], "processing_urgents() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_urgents", false]], "qc (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.qc", false]], "qc() (in module histopath_bim_des.process.p80_qc)": [[23, "histopath_bim_des.process.p80_qc.qc", false]], "qc_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.qc_staff", false]], "qc_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.qc_staff", false]], "rates (histopath_bim_des.config.arrivals.arrivalschedule attribute)": [[3, "histopath_bim_des.config.arrivals.ArrivalSchedule.rates", false]], "receive_and_sort (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.receive_and_sort", false]], "receive_and_sort (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.receive_and_sort", false]], "reception (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.reception", false]], "reception_cutup (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.reception_cutup", false]], "reception_cutup (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.reception_cutup", false]], "register_process() (in module histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.register_process", false]], "register_processes() (in module histopath_bim_des.process.p10_reception)": [[16, "histopath_bim_des.process.p10_reception.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p20_cutup)": [[17, "histopath_bim_des.process.p20_cutup.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p40_microtomy)": [[19, "histopath_bim_des.process.p40_microtomy.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p60_labelling)": [[21, "histopath_bim_des.process.p60_labelling.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p80_qc)": [[23, "histopath_bim_des.process.p80_qc.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p90_reporting)": [[24, "histopath_bim_des.process.p90_reporting.register_processes", false]], "remove_table_filters() (in module histopath_bim_des.excel)": [[12, "histopath_bim_des.excel.remove_table_filters", false]], "report() (in module histopath_bim_des.process.p90_reporting)": [[24, "histopath_bim_des.process.p90_reporting.report", false]], "resource (histopath_bim_des.process.core.resourcescheduler attribute)": [[15, "histopath_bim_des.process.core.ResourceScheduler.resource", false]], "resource_allocation_interval_hours (in module histopath_bim_des.util)": [[26, "histopath_bim_des.util.RESOURCE_ALLOCATION_INTERVAL_HOURS", false]], "resourceinfo (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourceInfo", false]], "resources (class in histopath_bim_des.model)": [[13, "histopath_bim_des.model.Resources", false]], "resources (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.resources", false]], "resources (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.resources", false]], "resourceschedule (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourceSchedule", false]], "resourcescheduler (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.ResourceScheduler", false]], "resourcesinfo (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourcesInfo", false]], "retur (histopath_bim_des.process.core.runnerdurations attribute)": [[15, "histopath_bim_des.process.core.RunnerDurations.retur", false]], "routine (histopath_bim_des.specimens.priority attribute)": [[25, "histopath_bim_des.specimens.Priority.ROUTINE", false]], "run() (histopath_bim_des.model.model method)": [[13, "histopath_bim_des.model.Model.run", false]], "runner (histopath_bim_des.process.core.deliveryprocess attribute)": [[15, "histopath_bim_des.process.core.DeliveryProcess.runner", false]], "runner_speed (histopath_bim_des.config.runners.runnerconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerConfig.runner_speed", false]], "runner_times (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.runner_times", false]], "runner_times() (in module histopath_bim_des.bim)": [[1, "histopath_bim_des.bim.runner_times", false]], "runnerconfig (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerConfig", false]], "runnerdurations (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.RunnerDurations", false]], "runnerextradurations (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerExtraDurations", false]], "runnertimes (class in histopath_bim_des.model)": [[13, "histopath_bim_des.model.RunnerTimes", false]], "runnertimesconfig (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig", false]], "sample() (histopath_bim_des.distribution.intpert method)": [[11, "histopath_bim_des.distribution.IntPERT.sample", false]], "sample() (histopath_bim_des.distribution.inttri method)": [[11, "histopath_bim_des.distribution.IntTri.sample", false]], "sample() (histopath_bim_des.distribution.pert method)": [[11, "histopath_bim_des.distribution.PERT.sample", false]], "scanning (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.scanning", false]], "scanning_generic() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_generic", false]], "scanning_machine_megas (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.scanning_machine_megas", false]], "scanning_machine_megas (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.scanning_machine_megas", false]], "scanning_machine_regular (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.scanning_machine_regular", false]], "scanning_machine_regular (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.scanning_machine_regular", false]], "scanning_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.scanning_megas", false]], "scanning_megas (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.scanning_megas", false]], "scanning_megas() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_megas", false]], "scanning_qc (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.scanning_qc", false]], "scanning_qc (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.scanning_qc", false]], "scanning_regular (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.scanning_regular", false]], "scanning_regular (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.scanning_regular", false]], "scanning_regular() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_regular", false]], "scanning_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.scanning_staff", false]], "scanning_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.scanning_staff", false]], "scanning_start() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_start", false]], "schedule (histopath_bim_des.config.resources.resourceinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourceInfo.schedule", false]], "schedule (histopath_bim_des.process.core.resourcescheduler attribute)": [[15, "histopath_bim_des.process.core.ResourceScheduler.schedule", false]], "setup() (histopath_bim_des.model.model method)": [[13, "histopath_bim_des.model.Model.setup", false]], "setup() (histopath_bim_des.process.core.arrivalgenerator method)": [[15, "histopath_bim_des.process.core.ArrivalGenerator.setup", false]], "setup() (histopath_bim_des.process.core.baseprocess method)": [[15, "histopath_bim_des.process.core.BaseProcess.setup", false]], "setup() (histopath_bim_des.process.core.batchingprocess method)": [[15, "histopath_bim_des.process.core.BatchingProcess.setup", false]], "setup() (histopath_bim_des.process.core.collationprocess method)": [[15, "histopath_bim_des.process.core.CollationProcess.setup", false]], "setup() (histopath_bim_des.process.core.deliveryprocess method)": [[15, "histopath_bim_des.process.core.DeliveryProcess.setup", false]], "setup() (histopath_bim_des.process.core.process method)": [[15, "histopath_bim_des.process.core.Process.setup", false]], "setup() (histopath_bim_des.process.core.resourcescheduler method)": [[15, "histopath_bim_des.process.core.ResourceScheduler.setup", false]], "setup() (histopath_bim_des.specimens.batch method)": [[25, "histopath_bim_des.specimens.Batch.setup", false]], "setup() (histopath_bim_des.specimens.block method)": [[25, "histopath_bim_des.specimens.Block.setup", false]], "setup() (histopath_bim_des.specimens.slide method)": [[25, "histopath_bim_des.specimens.Slide.setup", false]], "setup() (histopath_bim_des.specimens.specimen method)": [[25, "histopath_bim_des.specimens.Specimen.setup", false]], "shapelymodel (class in histopath_bim_des.bim)": [[1, "histopath_bim_des.bim.ShapelyModel", false]], "shortest_path() (histopath_bim_des.bim.shapelymodel method)": [[1, "histopath_bim_des.bim.ShapelyModel.shortest_path", false]], "sim_hours (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.sim_hours", false]], "sim_length (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.sim_length", false]], "slide (class in histopath_bim_des.specimens)": [[25, "histopath_bim_des.specimens.Slide", false]], "specimen (class in histopath_bim_des.specimens)": [[25, "histopath_bim_des.specimens.Specimen", false]], "specimen_data (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.specimen_data", false]], "staining (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.staining", 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"histopath_bim_des.process.core module", "histopath_bim_des.process.p10_reception module", "histopath_bim_des.process.p20_cutup module", "histopath_bim_des.process.p30_processing module", "histopath_bim_des.process.p40_microtomy module", "histopath_bim_des.process.p50_staining module", "histopath_bim_des.process.p60_labelling module", "histopath_bim_des.process.p70_scanning module", "histopath_bim_des.process.p80_qc module", "histopath_bim_des.process.p90_reporting module", "histopath_bim_des.specimens module", "histopath_bim_des.util module", "histopath_bim_des", "Model Configuration", "BIM-DES integration demo", "Histopathology processes", "Simulation and KPI extraction"], "titleterms": {"api": 29, "arriv": 3, "batch": 4, "bim": [1, 29], "config": [2, 3, 4, 5, 6, 7, 8, 9, 10], "configur": 28, "content": [0, 2, 14, 29], "core": 15, "de": 29, "demo": 29, "distribut": [6, 11], "excel": 12, "extract": 31, "gener": 28, "global_var": 7, "histopath_bim_d": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27], "histopathologi": 30, "indic": 29, "integr": 29, "kpi": 31, "model": [13, 28], "modul": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26], "p10_recept": 16, "p20_cutup": 17, "p30_process": 18, "p40_microtomi": 19, "p50_stain": 20, "p60_label": 21, "p70_scan": 22, "p80_qc": 23, "p90_report": 24, "packag": [0, 2, 14], "process": [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30], "refer": 29, "resourc": 8, "runner": [9, 28], "simul": 31, "specimen": 25, "submodul": [0, 2, 14], "subpackag": 0, "tabl": 29, "task": 10, "time": 28, "util": 26}}) \ No newline at end of file +Search.setIndex({"alltitles": {"BIM-DES integration demo": [[29, "bim-des-integration-demo"]], "Generating a runner times configuration": [[28, "generating-a-runner-times-configuration"]], "Histopathology processes": [[31, "histopathology-processes"]], "Installation": [[30, "installation"]], "Model 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"histopath_bim_des.config.global_vars.Globals.num_slides_levels", false]], "num_slides_levels (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.num_slides_levels", false]], "num_slides_megas (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.num_slides_megas", false]], "num_slides_megas (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.num_slides_megas", false]], "num_slides_serials (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.num_slides_serials", false]], "num_slides_serials (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.num_slides_serials", false]], "out (histopath_bim_des.process.core.runnerdurations attribute)": [[15, "histopath_bim_des.process.core.RunnerDurations.out", false]], "out_process (histopath_bim_des.process.core.batchingprocess attribute)": [[15, "histopath_bim_des.process.core.BatchingProcess.out_process", false]], "out_process (histopath_bim_des.process.core.collationprocess attribute)": [[15, "histopath_bim_des.process.core.CollationProcess.out_process", false]], "out_process (histopath_bim_des.process.core.deliveryprocess attribute)": [[15, "histopath_bim_des.process.core.DeliveryProcess.out_process", false]], "parent (histopath_bim_des.specimens.component attribute)": [[25, "histopath_bim_des.specimens.Component.parent", false]], "path (histopath_bim_des.config.runners.pathdefinition attribute)": [[9, "histopath_bim_des.config.runners.PathDefinition.path", false]], "pathdefinition (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.PathDefinition", false]], "pert (class in histopath_bim_des.distribution)": [[11, "histopath_bim_des.distribution.PERT", false]], "pert (histopath_bim_des.distribution.intpert attribute)": [[11, "histopath_bim_des.distribution.IntPERT.pert", false]], "plot_floor() (histopath_bim_des.bim.shapelymodel method)": [[1, "histopath_bim_des.bim.ShapelyModel.plot_floor", false]], "post_processing() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.post_processing", false]], "post_scanning() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.post_scanning", false]], "post_staining() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.post_staining", false]], "pre_booking_in_investigation (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.pre_booking_in_investigation", false]], "pre_booking_in_investigation (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.pre_booking_in_investigation", false]], "print_info() (histopath_bim_des.distribution.pert method)": [[11, "histopath_bim_des.distribution.PERT.print_info", false]], "prio (histopath_bim_des.specimens.component attribute)": [[25, "histopath_bim_des.specimens.Component.prio", false]], "priority (class in histopath_bim_des.specimens)": [[25, "histopath_bim_des.specimens.Priority", false]], "priority (histopath_bim_des.specimens.priority attribute)": [[25, "histopath_bim_des.specimens.Priority.PRIORITY", false]], "prob_bms_cutup (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_bms_cutup", false]], "prob_bms_cutup (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_bms_cutup", false]], "prob_bms_cutup_urgent (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_bms_cutup_urgent", false]], "prob_bms_cutup_urgent (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_bms_cutup_urgent", false]], "prob_decalc_bone (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_decalc_bone", false]], "prob_decalc_bone (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_decalc_bone", false]], "prob_decalc_oven (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_decalc_oven", false]], "prob_decalc_oven (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_decalc_oven", false]], "prob_internal (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_internal", false]], "prob_internal (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_internal", false]], "prob_invest_easy (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_invest_easy", false]], "prob_invest_easy (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_invest_easy", false]], "prob_invest_external (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_invest_external", false]], "prob_invest_external (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_invest_external", false]], "prob_invest_hard (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_invest_hard", false]], "prob_invest_hard (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_invest_hard", false]], "prob_large_cutup (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_large_cutup", false]], "prob_large_cutup (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_large_cutup", false]], "prob_large_cutup_urgent (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_large_cutup_urgent", false]], "prob_large_cutup_urgent (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_large_cutup_urgent", false]], "prob_mega_blocks (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_mega_blocks", false]], "prob_mega_blocks (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_mega_blocks", false]], "prob_microtomy_levels (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_microtomy_levels", false]], "prob_microtomy_levels (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_microtomy_levels", false]], "prob_pool_cutup (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_pool_cutup", false]], "prob_pool_cutup (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_pool_cutup", false]], "prob_pool_cutup_urgent (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_pool_cutup_urgent", false]], "prob_pool_cutup_urgent (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_pool_cutup_urgent", false]], "prob_prebook (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_prebook", false]], "prob_prebook (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_prebook", false]], "prob_priority_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_priority_cancer", false]], "prob_priority_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_priority_cancer", false]], "prob_priority_non_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_priority_non_cancer", false]], "prob_priority_non_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_priority_non_cancer", false]], "prob_urgent_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_urgent_cancer", false]], "prob_urgent_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_urgent_cancer", false]], "prob_urgent_non_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_urgent_non_cancer", false]], "prob_urgent_non_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_urgent_non_cancer", false]], "process (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.Process", false]], "process() (histopath_bim_des.process.core.arrivalgenerator method)": [[15, "histopath_bim_des.process.core.ArrivalGenerator.process", false]], "process() (histopath_bim_des.process.core.baseprocess method)": [[15, "histopath_bim_des.process.core.BaseProcess.process", false]], "process() (histopath_bim_des.process.core.batchingprocess method)": [[15, "histopath_bim_des.process.core.BatchingProcess.process", false]], "process() (histopath_bim_des.process.core.collationprocess method)": [[15, "histopath_bim_des.process.core.CollationProcess.process", false]], "process() (histopath_bim_des.process.core.deliveryprocess method)": [[15, "histopath_bim_des.process.core.DeliveryProcess.process", false]], "process() (histopath_bim_des.process.core.process method)": [[15, "histopath_bim_des.process.core.Process.process", false]], "process() (histopath_bim_des.process.core.resourcescheduler method)": [[15, "histopath_bim_des.process.core.ResourceScheduler.process", false]], "process() (histopath_bim_des.specimens.specimen method)": [[25, "histopath_bim_des.specimens.Specimen.process", false]], "processdoormap (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap", false]], "processes (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.processes", false]], "processing (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.processing", false]], "processing_assign_queue() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_assign_queue", false]], "processing_generic() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_generic", false]], "processing_large_surgicals (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_large_surgicals", false]], "processing_large_surgicals (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_large_surgicals", false]], "processing_larges() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_larges", false]], "processing_machine (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.processing_machine", false]], "processing_machine (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.processing_machine", false]], "processing_megas (histopath_bim_des.config.batching.batchsizes attribute)": [[4, "histopath_bim_des.config.batching.BatchSizes.processing_megas", false]], "processing_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_megas", false]], "processing_megas (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_megas", false]], "processing_megas() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_megas", false]], "processing_microtomy (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.processing_microtomy", false]], "processing_microtomy (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.processing_microtomy", false]], "processing_regular (histopath_bim_des.config.batching.batchsizes attribute)": [[4, "histopath_bim_des.config.batching.BatchSizes.processing_regular", false]], "processing_room_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.processing_room_staff", false]], "processing_room_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.processing_room_staff", false]], "processing_small_surgicals (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_small_surgicals", false]], "processing_small_surgicals (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_small_surgicals", false]], "processing_smalls() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_smalls", false]], "processing_start() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_start", false]], "processing_urgent (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_urgent", false]], "processing_urgent (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_urgent", false]], "processing_urgents() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_urgents", false]], "qc (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.qc", false]], "qc() (in module histopath_bim_des.process.p80_qc)": [[23, "histopath_bim_des.process.p80_qc.qc", false]], "qc_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.qc_staff", false]], "qc_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.qc_staff", false]], "rates (histopath_bim_des.config.arrivals.arrivalschedule attribute)": [[3, "histopath_bim_des.config.arrivals.ArrivalSchedule.rates", false]], "receive_and_sort (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.receive_and_sort", false]], "receive_and_sort (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.receive_and_sort", false]], "reception (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.reception", false]], "reception_cutup (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.reception_cutup", false]], "reception_cutup (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.reception_cutup", false]], "register_process() (in module histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.register_process", false]], "register_processes() (in module histopath_bim_des.process.p10_reception)": [[16, "histopath_bim_des.process.p10_reception.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p20_cutup)": [[17, "histopath_bim_des.process.p20_cutup.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p40_microtomy)": [[19, "histopath_bim_des.process.p40_microtomy.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p60_labelling)": [[21, "histopath_bim_des.process.p60_labelling.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p80_qc)": [[23, "histopath_bim_des.process.p80_qc.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p90_reporting)": [[24, "histopath_bim_des.process.p90_reporting.register_processes", false]], "remove_table_filters() (in module histopath_bim_des.excel)": [[12, "histopath_bim_des.excel.remove_table_filters", false]], "report() (in module histopath_bim_des.process.p90_reporting)": [[24, "histopath_bim_des.process.p90_reporting.report", false]], "resource (histopath_bim_des.process.core.resourcescheduler attribute)": [[15, "histopath_bim_des.process.core.ResourceScheduler.resource", false]], "resource_allocation_interval_hours (in module histopath_bim_des.util)": [[26, "histopath_bim_des.util.RESOURCE_ALLOCATION_INTERVAL_HOURS", false]], "resourceinfo (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourceInfo", false]], "resources (class in histopath_bim_des.model)": [[13, "histopath_bim_des.model.Resources", false]], "resources (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.resources", false]], "resources (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.resources", false]], "resourceschedule (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourceSchedule", false]], "resourcescheduler (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.ResourceScheduler", false]], "resourcesinfo (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourcesInfo", false]], "retur (histopath_bim_des.process.core.runnerdurations attribute)": [[15, "histopath_bim_des.process.core.RunnerDurations.retur", false]], "routine (histopath_bim_des.specimens.priority attribute)": [[25, "histopath_bim_des.specimens.Priority.ROUTINE", false]], "run() (histopath_bim_des.model.model method)": [[13, "histopath_bim_des.model.Model.run", false]], "runner (histopath_bim_des.process.core.deliveryprocess attribute)": [[15, "histopath_bim_des.process.core.DeliveryProcess.runner", false]], "runner_speed (histopath_bim_des.config.runners.runnerconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerConfig.runner_speed", false]], "runner_times (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.runner_times", false]], "runner_times() (in module histopath_bim_des.bim)": [[1, "histopath_bim_des.bim.runner_times", false]], "runnerconfig (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerConfig", false]], "runnerdurations (class in 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"version": 30, "via": 32, "visual": 31, "w": 12, "wa": [10, 30], "wall": [0, 1], "wall_shap": [0, 1], "want": 13, "wax": [10, 18, 25], "wbook": [3, 4, 5, 7, 8, 9, 10, 12, 32], "we": 32, "week": [3, 8], "weekend": 18, "weight": 1, "when": [1, 13], "where": [1, 9], "whether": [8, 13], "which": [12, 13, 15, 26, 29, 32], "while": 13, "wiki": 11, "wikipedia": 11, "wip": [0, 13, 27], "within": [25, 29], "without": 1, "work": [13, 15], "workbook": [3, 4, 5, 7, 8, 9, 10, 12], "worksheet": [12, 28], "write": [10, 12, 24, 32], "write_report": [0, 2, 10, 13], "write_t": [0, 12, 27, 28], "xlsx": [28, 32], "yet": 25, "yield": 15, "yin": 29, "yinchi": 30, "you": [13, 30], "your": 32}, "titles": ["histopath_bim_des package", "histopath_bim_des.bim module", "histopath_bim_des.config package", "histopath_bim_des.config.arrivals module", "histopath_bim_des.config.batching module", "histopath_bim_des.config.config module", "histopath_bim_des.config.distributions module", "histopath_bim_des.config.global_vars module", "histopath_bim_des.config.resources module", "histopath_bim_des.config.runners module", "histopath_bim_des.config.tasks module", "histopath_bim_des.distribution module", "histopath_bim_des.excel module", "histopath_bim_des.model module", "histopath_bim_des.process package", "histopath_bim_des.process.core module", "histopath_bim_des.process.p10_reception module", "histopath_bim_des.process.p20_cutup module", "histopath_bim_des.process.p30_processing module", "histopath_bim_des.process.p40_microtomy module", "histopath_bim_des.process.p50_staining module", "histopath_bim_des.process.p60_labelling module", "histopath_bim_des.process.p70_scanning module", "histopath_bim_des.process.p80_qc module", "histopath_bim_des.process.p90_reporting module", "histopath_bim_des.specimens module", "histopath_bim_des.util module", "histopath_bim_des", "Model Configuration", "BIM-DES integration demo", "Installation", "Histopathology processes", "Simulation and KPI extraction", "Third-party libraries"], "titleterms": {"arriv": 3, "batch": 4, "bim": [1, 29], "config": [2, 3, 4, 5, 6, 7, 8, 9, 10], "configur": 28, "content": [0, 2, 14], "core": 15, "de": 29, "demo": 29, "distribut": [6, 11], "excel": 12, "extract": 32, "gener": 28, "global_var": 7, "histopath_bim_d": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27], "histopathologi": 31, "instal": 30, "integr": 29, "kpi": 32, "librari": 33, "model": [13, 28], "modul": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26], "p10_recept": 16, "p20_cutup": 17, "p30_process": 18, "p40_microtomi": 19, "p50_stain": 20, "p60_label": 21, "p70_scan": 22, "p80_qc": 23, "p90_report": 24, "packag": [0, 2, 14], "parti": 33, "process": [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31], "resourc": 8, "runner": [9, 28], "simul": 32, "specimen": 25, "submodul": [0, 2, 14], "subpackag": 0, "task": 10, "third": 33, "time": 28, "util": 26}}) \ No newline at end of file diff --git a/docs/html/simulation.html b/docs/html/simulation.html index c6ed4aa..7b99e5f 100644 --- a/docs/html/simulation.html +++ b/docs/html/simulation.html @@ -46,14 +46,25 @@ @@ -72,7 +83,7 @@
  • Simulation and KPI extraction
  • - View page source + Edit on GitHub
    • diff --git a/docs/html/thirdparty.html b/docs/html/thirdparty.html new file mode 100644 index 0000000..7768eba --- /dev/null +++ b/docs/html/thirdparty.html @@ -0,0 +1,153 @@ + + + + + + + Third-party libraries — histopath-bim-des 0.0.0 documentation + + + + + + + + + + + + + + + + + + + +
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    Third-party libraries

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    This project depends on a number of third-party Python libraries:

    +

    General:

    + +

    BIM integration:

    + +

    Data analysis:

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    • openpyxl: Excel file API

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    • pandas: dataframes

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    • scipy: scientific computing (statistics, optimisation, linear algebra…)

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    Data representation and validation:

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    • pydantic: dataclasses with validation

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    • dacite: construct Python dataclasses from dicts

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    For a full list of libraries, see the project’s pyproject.toml file.

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    + + + + \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 738517a..6d8f5d7 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -3,8 +3,9 @@ BIM-DES integration demo **Authors:** -* Yin-Chi Chan, Institute for Manufacturing, University of Cambridge (maintainer) -* Nicola Moretti, Bartlett School of Sustainable Construction, University College London +* `Yin-Chi Chan `_, + Institute for Manufacturing, University of Cambridge (maintainer) +* `Nicola Moretti `_, Bartlett School of Sustainable Construction, University College London This Python package contains code for a BIM-DES (building information modelling and discrete event simulation) integration model of the histopathology lab at Addenbrooke's Hospital, Cambridge, UK. @@ -16,26 +17,39 @@ as the proportion of specimens completed within a given number of days. By enabling or disabling pathways in the parsed .ifc file, different runner times will be calculated, resulting in different performance with respect to the key performance indicators (KPIs) such as mean lab turnaround time (TAT) and service level (% of lab TAT less than *N* days). -Examples can be found in the ``notebooks/`` directory of this project. +Examples can be found in the `notebooks/ `_ directory of this project. + .. toctree:: :maxdepth: 2 :caption: Contents + :hidden: + Jupyter notebooks πŸ”— config simulation processes - Jupyter notebooks .. toctree:: :maxdepth: 2 - :caption: API reference: + :caption: Technical + :hidden: + + Installation ⬇️ + Third-party libraries πŸ“š + +.. toctree:: + :maxdepth: 2 + :caption: API reference πŸ“– + :hidden: apidoc/histopath_bim_des -Indices and tables -================== +.. toctree:: + :maxdepth: 0 + :caption: Indicies and Tables πŸ” + :hidden: -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` + genindex + modindex + search diff --git a/docs/installation.md b/docs/installation.md new file mode 100644 index 0000000..1627dda --- /dev/null +++ b/docs/installation.md @@ -0,0 +1,33 @@ +# Installation + +This project was developed using the [Poetry](https://python-poetry.org/) package manager and +Python 3.12. To install the Python package and its dependencies, the following bash scripts can +be used: + +```bash +pip install poetry +``` +**OR** +```bash +sudo apt-get install python3-poetry +``` + +The second form is necessary if the pip option returns an +"`This environment is externally managed`" error. + +```bash +git clone https://github.com/yinchi/histopath-bim-des +cd histopath-bim-des + +# if you have obtained a copy of histo.ifc +mkdir -p assets/private/ +cp /path/to/histo.ifc assets/private/ + +# required by erdantic +sudo apt install libgraphviz-dev + +# If 3.12 is not the default Python version +poetry venv use /usr/bin/python3/12 + +poetry install +``` diff --git a/docs/thirdparty.md b/docs/thirdparty.md new file mode 100644 index 0000000..395b35a --- /dev/null +++ b/docs/thirdparty.md @@ -0,0 +1,28 @@ +# Third-party libraries + +This project depends on a number of third-party Python libraries: + +**General:** + +* [poetry](https://python-poetry.org/): package manager +* [salabim](https://www.salabim.org/): discrete-event simulation + +**BIM integration:** + +* [ifcopenshell](https://ifcopenshell.org/): Industry Foundation Classes +* [networkx](https://networkx.org/): graph/network analysis +* [shapely](https://shapely.readthedocs.io/): geometric analysis + + +**Data analysis:** + +* [openpyxl](https://openpyxl.readthedocs.io/): Excel file API +* [pandas](https://pandas.pydata.org/): dataframes +* [scipy](https://scipy.org/): scientific computing (statistics, optimisation, linear algebra...) + +**Data representation and validation:** + +* [pydantic](https://docs.pydantic.dev/): dataclasses with validation +* [dacite](https://github.com/konradhalas/dacite/): construct Python dataclasses from dicts + +For a full list of libraries, see the project's `pyproject.toml` file.