diff --git a/docs/html/processes.html b/docs/html/processes.html
index 73ac098..2e62cd2 100644
--- a/docs/html/processes.html
+++ b/docs/html/processes.html
@@ -49,6 +49,7 @@
Model Configuration
Simulation and KPI extraction
Histopathology processes
+
`Jupyter notebooks <https://github.com/yinchi/histopath-bim-des/tree/main/notebooks>`_
API reference:
API reference:
API reference:
diff --git a/docs/html/searchindex.js b/docs/html/searchindex.js
index 774e31e..5bc5d49 100644
--- a/docs/html/searchindex.js
+++ b/docs/html/searchindex.js
@@ -1 +1 @@
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"histopath_bim_des.config.global_vars.Globals.num_slides_larges", false]], "num_slides_larges (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.num_slides_larges", false]], "num_slides_levels (histopath_bim_des.config.global_vars.globals attribute)": [[7, "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, 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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
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"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", false]], "staining_labelling (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.staining_labelling", false]], "staining_labelling (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.staining_labelling", false]], "staining_machine (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.staining_machine", false]], "staining_machine (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.staining_machine", false]], "staining_megas (histopath_bim_des.config.batching.batchsizes attribute)": [[4, "histopath_bim_des.config.batching.BatchSizes.staining_megas", false]], "staining_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.staining_megas", false]], "staining_megas (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.staining_megas", false]], "staining_megas() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.staining_megas", false]], "staining_regular (histopath_bim_des.config.batching.batchsizes attribute)": [[4, "histopath_bim_des.config.batching.BatchSizes.staining_regular", false]], "staining_regular (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.staining_regular", false]], "staining_regular (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.staining_regular", false]], "staining_regular() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.staining_regular", false]], "staining_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.staining_staff", false]], "staining_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.staining_staff", false]], "staining_start() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.staining_start", false]], "task_durations (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.task_durations", false]], "task_durations (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.task_durations", false]], "taskdurations (class in histopath_bim_des.model)": [[13, "histopath_bim_des.model.TaskDurations", false]], "taskdurationsinfo (class in histopath_bim_des.config.tasks)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo", false]], "time_unit (histopath_bim_des.config.distributions.distributioninfo attribute)": [[6, "histopath_bim_des.config.distributions.DistributionInfo.time_unit", false]], "timestamp() (histopath_bim_des.specimens.specimen method)": [[25, "histopath_bim_des.specimens.Specimen.timestamp", false]], "to_shapely() (histopath_bim_des.bim.bimmodel method)": [[1, "histopath_bim_des.bim.BimModel.to_shapely", false]], "total (histopath_bim_des.model.wips attribute)": [[13, "histopath_bim_des.model.Wips.total", false]], "tri (class in histopath_bim_des.distribution)": [[11, "histopath_bim_des.distribution.Tri", false]], "tri (histopath_bim_des.distribution.inttri attribute)": [[11, "histopath_bim_des.distribution.IntTri.tri", false]], "type (histopath_bim_des.config.distributions.distributioninfo attribute)": [[6, "histopath_bim_des.config.distributions.DistributionInfo.type", false]], "type (histopath_bim_des.config.distributions.intdistributioninfo attribute)": [[6, "histopath_bim_des.config.distributions.IntDistributionInfo.type", false]], "type (histopath_bim_des.config.resources.resourceinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourceInfo.type", false]], "unload (histopath_bim_des.process.core.runnerdurations attribute)": [[15, "histopath_bim_des.process.core.RunnerDurations.unload", false]], "unload_bone_station (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_bone_station", false]], "unload_bone_station (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_bone_station", false]], "unload_coverslip_machine_regular (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_coverslip_machine_regular", false]], "unload_coverslip_machine_regular (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_coverslip_machine_regular", false]], "unload_from_decalc_oven (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_from_decalc_oven", false]], "unload_from_decalc_oven (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_from_decalc_oven", false]], "unload_processing_machine (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_processing_machine", false]], "unload_processing_machine (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_processing_machine", false]], "unload_scanning_machine_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_scanning_machine_megas", false]], "unload_scanning_machine_megas (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_scanning_machine_megas", false]], "unload_scanning_machine_regular (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_scanning_machine_regular", false]], "unload_scanning_machine_regular (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_scanning_machine_regular", false]], "unload_staining_machine_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_staining_machine_megas", false]], 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"processing_large_surg": [0, 2, 10, 13], "processing_machin": [0, 2, 8, 13], "processing_mega": [0, 2, 4, 10, 13, 14, 18], "processing_microtomi": [0, 2, 9, 13], "processing_regular": [2, 4], "processing_room_staff": [0, 2, 8, 13], "processing_smal": [0, 14, 18], "processing_small_surg": [0, 2, 10, 13], "processing_start": [0, 14, 18], "processing_urg": [0, 2, 10, 13, 14, 18], "produc": [7, 10, 17, 25], "program": 18, "programm": 10, "progress": 13, "project": [28, 29, 30], "proport": [29, 31], "provid": [1, 11], "push": 15, "pydant": 5, "python": [28, 29], "qc": [0, 2, 4, 9, 14, 23], "qc_end": 31, "qc_staff": [0, 2, 8, 13], "qualiti": [10, 23], "qualnam": 25, "queue": [15, 17, 18, 25], "rais": 1, "random": [6, 11, 17], "randomstream": 11, "rang": [7, 12, 31], "rate": [2, 3, 15, 26], "re": 31, "reactiv": 13, "read": 12, "reason": 1, "receiv": [10, 15], "receive_and_sort": [0, 2, 10, 13], "recept": [2, 4, 9, 10, 16], "reception_cutup": [0, 2, 9, 13], "reception_start": 31, "reconstitut": 15, "reduc": 18, "regist": [15, 16, 17, 18, 19, 20, 21, 22, 23, 24], "register_process": [0, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24], "regular": [4, 10, 20, 22], "relat": [1, 9], "relationship": 28, "remain": 7, "remov": [8, 12], "remove_table_filt": [0, 12, 27], "replac": [11, 12], "replic": 13, "report": [0, 10, 14, 24], "reporting_end": 31, "repres": [1, 6], "represent": [1, 11, 30], "requir": [1, 7, 10, 15, 28, 31], "reset_index": 12, "resourc": [0, 2, 5, 13, 14, 15, 17, 26, 27, 31], "resource_allocation_interval_hour": [0, 15, 26, 27], "resourceinfo": [0, 2, 8], "resourceschedul": [0, 2, 8, 14, 15], "resourcesinfo": [0, 2, 5, 8], "respect": 29, "respons": 15, "result": 29, "retur": [14, 15], "return": [1, 3, 4, 5, 7, 8, 9, 10, 11, 12], "right": 1, "room": [9, 17], "routin": [0, 25], "row": [3, 4, 8, 10], "row_nam": 8, "rt": 28, "run": [0, 5, 13, 31], "runner": [0, 1, 2, 5, 13, 14, 15, 29], "runner_cfg_path": 28, "runner_spe": [2, 5, 9, 31], "runner_tim": [0, 1, 2, 5, 27, 28], "runnerconfig": [0, 1, 2, 9, 28], "runnerdur": [0, 14, 15], "runnerextradur": [0, 2, 9], "runnertim": [0, 13, 27], "runnertimesconfig": [0, 2, 5, 9, 29], "salabim": [11, 15, 25, 31], "same": [4, 13, 15], "sampl": [0, 11, 13], "save": 25, "scan": [2, 4, 8, 9, 10, 22], "scanning_gener": [0, 14, 22], "scanning_machine_mega": [0, 2, 8, 13], "scanning_machine_regular": [0, 2, 8, 13], "scanning_mega": [0, 2, 10, 13, 14, 22], "scanning_qc": [0, 2, 9, 13], "scanning_regular": [0, 2, 10, 13, 14, 22], "scanning_staff": [0, 2, 8, 13], "scanning_start": [0, 14, 22], "scenario": 28, "schedul": [2, 3, 8, 13, 14, 15], "school": 29, "script": 28, "search": [1, 29], "second": [1, 6], "section": 10, "see": [11, 13], "select": 1, "self": [1, 5, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25], "send": [18, 20], "separ": 20, "sequenc": [3, 8, 9], "serial": [7, 10], "serialis": 13, "servic": 29, "set": [8, 13, 15, 25, 28], "setup": [0, 13, 14, 15, 25], "seven": 3, "shape": 1, "shapelymodel": [0, 1, 27], "sheet": 28, "sheet_nam": 12, "shortest": 1, "shortest_path": [0, 1], "should": 7, "shown": 28, "sim": [11, 13], "sim_hour": [2, 5, 31], "sim_length": [0, 13], "simpl": 31, "simplic": 17, "simul": [2, 3, 4, 5, 7, 8, 9, 10, 11, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29], "singl": [10, 12, 15, 17, 18, 28], "size": [1, 4, 10, 13, 15, 18, 20, 28], "skip_standbi": 25, "slide": [0, 4, 7, 10, 19, 20, 21, 22, 25, 27], "slip": 20, "small": [7, 10, 17, 18], "so": 13, "some": [9, 15], "sort": [13, 17], "sourc": [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25], "space": [7, 8], "special": [17, 18], "specifi": [13, 15, 28], "specimen": [0, 3, 4, 7, 10, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 29, 31], "specimen_data": [0, 13, 25, 31], "speed": [1, 5, 9], "split": 18, "staf": 10, "staff": [8, 15], "stage": [1, 9], "stain": [2, 4, 9, 10, 20], "staining_label": [0, 2, 9, 13], "staining_machin": [0, 2, 8, 13], "staining_mega": [0, 2, 4, 10, 13, 14, 20], "staining_regular": [0, 2, 4, 10, 13, 14, 20], "staining_staff": [0, 2, 8, 13], "staining_start": [0, 14, 20], "start": [1, 3, 6, 13, 18, 25], "static": [1, 3, 4, 5, 7, 8, 9, 10], "station": [4, 7, 10, 18], "statis": 31, "store": [7, 15], "storei": 1, "str": [1, 8, 9, 11, 12, 13, 15, 25], "string": [6, 11, 13], "studi": 1, "sub": 15, "submodul": [27, 29], "subpackag": [27, 29], "sun": 8, "suppress_pause_at_step": 25, "suppress_trac": 25, "surgic": [7, 10, 17, 18], "sustain": 29, "sy": 13, "symbol": 7, "system": [7, 16], "sytem": 10, "tab": [4, 8, 10], "tabl": 12, "tablerunnertim": 28, "take": [9, 15, 17, 18], "taken": 15, "task": [0, 2, 6, 7, 13, 17, 18, 20, 22], "task_dur": [0, 2, 5, 13], "taskdur": [0, 13, 27], "taskdurationsinfo": [0, 2, 5, 10], "tat": [29, 31], "templat": [8, 26], "textio": 11, "than": [11, 29], "thank": 31, "them": [1, 15], "themselv": 13, "therefor": 7, "thi": [4, 8, 10, 11, 13, 15, 25, 28, 29, 30], "three": [6, 11], "through": 1, "thu": 11, "till": 13, "time": [1, 5, 6, 9, 10, 13, 15, 18, 29, 31], "time_unit": [2, 6, 11], "timestamp": [0, 25, 31], "tissu": [10, 18, 25], "titl": [1, 4, 7, 10, 28], "to_door": 1, "to_shap": [0, 1], "todo": 18, "top": [1, 5], "top_right": 1, "total": [0, 13], "track": [3, 4, 8, 10, 13], "travel": [1, 9, 15], "tree": 29, "tri": [0, 11, 13, 27], "triangular": [6, 11], "trim": [10, 18], "true": [8, 13, 28, 31], "tupl": [1, 9], "turn": [25, 29], "turnaround": [29, 31], "two": [1, 9, 15], "type": [2, 4, 5, 6, 8, 9, 11, 13, 15, 17, 18, 25], "typic": [1, 15], "uk": [1, 29], "unbatch": 15, "underli": [6, 11], "underscor": 8, "unit": [6, 8, 17], "univers": 29, "unload": [9, 10, 14, 15], "unload_bone_st": [0, 2, 10, 13], "unload_coverslip_machine_regular": [0, 2, 10, 13], "unload_from_decalc_oven": [0, 2, 10, 13], "unload_processing_machin": [0, 2, 10, 13], "unload_scanning_machine_mega": [0, 2, 10, 13], "unload_scanning_machine_regular": [0, 2, 10, 13], "unload_staining_machine_mega": [0, 2, 10, 13], "unload_staining_machine_regular": [0, 2, 10, 13], "unloading_tim": [2, 9], "unstaf": 10, "up": [4, 7, 10, 13, 15, 17, 25], "updat": 18, "upon": 15, "urgenc": 13, "urgent": [0, 7, 10, 13, 18, 25], "us": [1, 7, 12, 13, 28, 29], "usuali": 13, "util": [0, 27], "utilis": 31, "v": 31, "valid": 6, "valu": [0, 3, 5, 6, 10, 11, 12, 13, 25, 31], "variabl": [7, 13], "variou": 13, "via": 31, "visual": 30, "w": 12, "wa": 10, "wall": [0, 1], "wall_shap": [0, 1], "want": 13, "wax": [10, 18, 25], "wbook": [3, 4, 5, 7, 8, 9, 10, 12, 31], "we": 31, "week": [3, 8], "weekend": 18, "weight": 1, "when": [1, 13], "where": [1, 9], "whether": [8, 13], "which": [12, 13, 15, 26, 29, 31], "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, 31], "write_report": [0, 2, 10, 13], "write_t": [0, 12, 27, 28], "xlsx": [28, 31], "yet": 25, "yield": 15, "yin": 29, "yinchi": 29, "you": 13, "your": 31}, "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", "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
diff --git a/docs/html/simulation.html b/docs/html/simulation.html
index 88e875f..8dceb71 100644
--- a/docs/html/simulation.html
+++ b/docs/html/simulation.html
@@ -49,6 +49,7 @@
- Model Configuration
- Simulation and KPI extraction
- Histopathology processes
+- `Jupyter notebooks <https://github.com/yinchi/histopath-bim-des/tree/main/notebooks>`_
API reference:
diff --git a/docs/index.rst b/docs/index.rst
index 70ffee4..3cb377b 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -25,6 +25,7 @@ Examples can be found in the ``notebooks/`` directory of this project.
config
simulation
processes
+ `Jupyter notebooks `_
.. toctree::
:maxdepth: 2
diff --git a/make.bat b/make.bat
deleted file mode 100644
index 32bb245..0000000
--- a/make.bat
+++ /dev/null
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
- set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
- echo.
- echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
- echo.installed, then set the SPHINXBUILD environment variable to point
- echo.to the full path of the 'sphinx-build' executable. Alternatively you
- echo.may add the Sphinx directory to PATH.
- echo.
- echo.If you don't have Sphinx installed, grab it from
- echo.https://www.sphinx-doc.org/
- exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
diff --git a/notebooks/plotting.ipynb b/notebooks/plotting.ipynb
index 045dcc3..fd0de1f 100644
--- a/notebooks/plotting.ipynb
+++ b/notebooks/plotting.ipynb
@@ -1,5 +1,15 @@
{
"cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Floor plans for the histopathology lab\n",
+ "\n",
+ "This notebook plots floor plans for the histopathology lab at Addenbrooke's Hospital, Cambridge,\n",
+ "UK."
+ ]
+ },
{
"cell_type": "code",
"execution_count": 1,
@@ -7,7 +17,6 @@
"outputs": [],
"source": [
"import matplotlib.pyplot as plt\n",
- "\n",
"from histopath_bim_des.bim import BimModel"
]
},
diff --git a/notebooks/runner_times_base.ipynb b/notebooks/runner_times_base.ipynb
index 4a94c01..7bfb7e3 100644
--- a/notebooks/runner_times_base.ipynb
+++ b/notebooks/runner_times_base.ipynb
@@ -4,7 +4,11 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Runner Times: base scenario"
+ "# Runner Times: base scenario\n",
+ "\n",
+ "THis notebook shows the connections between doors in the histopathology lab as a graph,\n",
+ "and computes the runner time between stages based on this logical graph, based on the given\n",
+ "configuration."
]
},
{
diff --git a/notebooks/runner_times_lift_down.ipynb b/notebooks/runner_times_lift_down.ipynb
index 9252dda..24718d6 100644
--- a/notebooks/runner_times_lift_down.ipynb
+++ b/notebooks/runner_times_lift_down.ipynb
@@ -4,7 +4,15 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Runner Times: lift-down scenario"
+ "# Runner Times: lift-down scenario\n",
+ "\n",
+ "\n",
+ "THis notebook shows the connections between doors in the histopathology lab as a graph,\n",
+ "and computes the runner time between stages based on this logical graph, based on the given\n",
+ "configuration.\n",
+ "\n",
+ "In this particular configuration, the lift is out of order, making the stairs the only connection\n",
+ "between Levels 3 and 4 (first and second floors) of the histopathology lab."
]
},
{