Add installed simpa version in hdf5 files

simpa/__init__.py

@@ -4,7 +4,13 @@
 
 from .utils import *
 from .log import Logger
+from importlib.metadata import version, PackageNotFoundError
 
+try:
+    __version__ = version("simpa")
+except PackageNotFoundError:
+    __version__ = "unknown version"
+
 from .core.simulation_modules.volume_creation_module.volume_creation_module_model_based_adapter import \
     ModelBasedVolumeCreationAdapter
 from .core.simulation_modules.volume_creation_module.volume_creation_module_segmentation_based_adapter import \

simpa/core/simulation.py

@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: MIT
 
 from simpa.utils import Tags
+from simpa import __version__
+
 from simpa.io_handling.io_hdf5 import save_hdf5, load_hdf5, save_data_field, load_data_field
 from simpa.io_handling.ipasc import export_to_ipasc
 from simpa.utils.settings import Settings
@@ -54,7 +56,8 @@ def simulate(simulation_pipeline: list, settings: Settings, digital_device_twin:
         simpa_output_path = path + settings[Tags.VOLUME_NAME]
 
     settings[Tags.SIMPA_OUTPUT_PATH] = simpa_output_path + ".hdf5"
-
+
+    simpa_output[Tags.SIMPA_VERSION] = __version__
     simpa_output[Tags.SETTINGS] = settings
     simpa_output[Tags.DIGITAL_DEVICE] = digital_device_twin
     simpa_output[Tags.SIMULATION_PIPELINE] = [type(x).__name__ for x in simulation_pipeline]

simpa/io_handling/io_hdf5.py

@@ -123,6 +123,8 @@ def data_grabber(file, path):
         """
 
         if isinstance(h5file[path], h5py._hl.dataset.Dataset):
+            if isinstance(h5file[path][()], bytes):
+                return h5file[path][()].decode("utf-8")
             return h5file[path][()]
 
         dictionary = {}

simpa/utils/dict_path_manager.py

@@ -16,7 +16,7 @@ def generate_dict_path(data_field, wavelength: (int, float) = None) -> str:
     :return: String which defines the path to the data_field.
     """
 
-    if data_field in [Tags.SIMULATIONS, Tags.SETTINGS, Tags.DIGITAL_DEVICE, Tags.SIMULATION_PIPELINE]:
+    if data_field in [Tags.SIMPA_VERSION, Tags.SIMULATIONS, Tags.SETTINGS, Tags.DIGITAL_DEVICE, Tags.SIMULATION_PIPELINE]:
         return "/" + data_field + "/"
 
     all_wl_independent_properties = wavelength_independent_properties + toolkit_tags

simpa/utils/tags.py

@@ -1256,7 +1256,7 @@ class Tags:
     Default filename of the SIMPA output if not specified otherwise.\n
     Usage: SIMPA package, naming convention
     """
-    SIMPA_VERSION = ("simpa_version", str)
+    SIMPA_VERSION = "simpa_version"
     """
     Version number of the currently installed simpa package
     Usage: SIMPA package