Json export step1 #281

nkrah · 2023-11-07T00:23:05Z

First steps of implementing a mechanism to dump/load a simulation as a JSON file.

add read-only option for properties; improve print output; implement from_dictionary(); implement to_json_string() and to_json_file(); iimplement create_gateobject_from_dict()

…r and PhysicsManager

…on_export_step1

…ateObject

…itions.py

…o_dictionary() and VolumeManager.to_dictionary()

…vel in dict

… archive if requested

… in Simulation.to_json_file()

…, not nested into dictionaries.

…and from_json_string()

nkrah · 2023-11-16T09:06:06Z

JSON export works for those parts of the simulation which already make use of the GateObject base class. Those are: VolumeManager and volumes, PhysicsManager, PhysicsListManager, Region, and now also Simulation.

The Simulation class has been refactored into a GateObject. User infos are now defined via the user_info_defaults class attribute. The SimulationUserInfo class has thus become obsolete and has been removed.

Using the json archiving option is simple, see test065_sim_as_dict.py.
The user activates it by setting the store_json_archive option in the simulation object to True.
When running the simulation, a json file containing all relevant parameters of the simulation will automatically be created and stored in the output directory which can be specified via the output_dir option of the simulation object.
The user can also manually call sim.to_json_file() to save the simulation as json file.

nkrah added 4 commits November 7, 2023 01:18

Initial implementation JSONEncoder

cb7b6f8

Create test065_sim_as_dict.py

04837f0

add as_dictionary() and dump_as_json_string() to GateObject

beac762

Initial implementation as_dictionary() in VolumeManager and Simulation

7190722

nkrah marked this pull request as draft November 7, 2023 00:23

nkrah added 25 commits November 9, 2023 22:45

Improve and enhance base.py:

18665a8

add read-only option for properties; improve print output; implement from_dictionary(); implement to_json_string() and to_json_file(); iimplement create_gateobject_from_dict()

Implement to_dictionary(), from_dictionary(), reset() in VolumeManage…

dabf93d

…r and PhysicsManager

Implement to_dictionary(), from_dictionary(), reset() in Region

e9db3ee

Implement JSON encoding for pathlib.Path

703b877

Add test065_sim_as_dict.py

0d343aa

English typo in comment

afbd4ba

Implement from_dictionary for BooleanVolumes

7221701

Merge branch 'master' of https://github.com/OpenGATE/opengate into js…

021eb01

…on_export_step1

Implement from_json_string and from_json_file in GateObject

1772047

Add test065_sim_from_dict.py

2761a04

Implement opengate.utility.find_all_paths_in_dict

f21a0bc

Make json indent=4 default

0766b0e

Turn Simulation into a GateObject; implement file archiving option

73cf6ec

move to_json and from_json methods to Simulation class

af780ff

update test065

391d424

update test065

c2d2dab

improve handling of outputdir in Simulation

1a86003

Implement opengate.utility.ensure_directory_exists

8ceae3b

Implement recursive_userinfo_to_dict() in base.py

18174e9

Adapt SourceEngine.create_g4_source_manager() to Simulation being a G…

11de279

…ateObject

set is_input_file flag in ImageVolume.image

24890b6

Implement recursive search through dictionaries

ecde9cf

Define __gate_dictionary_objects__ and __gate_list_objects__ in defin…

697dab1

…itions.py

Improve search for input files in Simulation; Update PhysicsManager.t…

04a57cc

…o_dictionary() and VolumeManager.to_dictionary()

Update GateJSONEncoder

7559d45

nkrah added 6 commits November 13, 2023 16:30

Remove utility.find_all_paths_in_dict - now in base.py

0548231

Update from_dictionary() method by including 'user_info' hierarchy le…

5c01cdf

…vel in dict

remove obsolete import in test065_sim_as_dict.py

de34566

Fix reference to visu user info of Simulation class

11cdbf4

Remove obsolete code from Simulation; let Simulation.run() store json…

7449246

… archive if requested

Enhance test007_volumes.py to store json archive

0a5fd35

nkrah marked this pull request as ready for review November 13, 2023 21:56

nkrah added 11 commits November 14, 2023 10:30

Improve utility.ensure_directory_exists: create also parents directories

d868c87

Implement Simulation.get_output_path() and improve file/path handling…

ff6b881

… in Simulation.to_json_file()

Minor update test065_sim_as_dict.py

324e9b5

Activate json archiving in test009_voxels.py

f88ffc3

Expose user_infos on visu and json storage in Simulation at top-level…

1bd082c

…, not nested into dictionaries.

Update path to json file in test065_sim_from_dict.py

371cc8d

Fix input file copying for mhd files

eaa8a3e

Avoid boilerplate code in SolidBoolean.from_dictionary()

889883d

Capture read-only properties in GateObject.from_dictionary()

9f1a109

Improve formatting of warning message in Simulation.from_json_file() …

78e084a

…and from_json_string()

Unclutter test065 and add assertion tests

8ee4f42

nkrah added 2 commits November 16, 2023 12:55

Improve test065 and let it run a simulation

73bfdec

remove unused import from test065_sim_from_dict.py

59128a2

nkrah merged commit 90fa3ea into OpenGATE:master Nov 16, 2023

nkrah deleted the json_export_step1 branch November 16, 2023 11:58

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Json export step1 #281

Json export step1 #281

nkrah commented Nov 7, 2023

nkrah commented Nov 16, 2023

Json export step1 #281

Json export step1 #281

Conversation

nkrah commented Nov 7, 2023

nkrah commented Nov 16, 2023