Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

T115 include bvf #182

Merged
merged 17 commits into from
Jul 29, 2024
Merged

T115 include bvf #182

merged 17 commits into from
Jul 29, 2024

Conversation

jnoelke
Copy link
Collaborator

@jnoelke jnoelke commented Oct 21, 2022

Code and tests

  • bvf is calcutated within the simulation and part of the hdf5 output
  • bvf calculation is tested for various scenarios
  • for all tissue types that include bvf and oxy we tested concistency between intially assigned values and calculations (We put it as part of TestCoreAssumptions but might also go somewhere else.)
  • For the tissue composition tests we added dummy values that might need to be adapted (another new issue?)

mschllnbrg and others added 5 commits August 17, 2022 15:22
@mschllnbrg
included blood volume fraction in output file:
1f399a8 
- new Tags.DATA_FIELD_BLOOD_VOLUME_FRACTION
- this tag is added to TissueProperties
- new function calculate_bvf
- calculate_bvf used in MolecularComposition
@jnoelke
test bvf
2c0e891 
- test calculation
- test comparison against lit values

ToDo:
- Consider cases with volume_fraction>1
- Add literature values for bvf
@jnoelke
Refactoring
bdf753f
@jnoelke
add bvf and sO2 consistency test
d345cf8
@mschllnbrg
Merge branch 'develop' into T115_include_bvf
4815b5c
@jnoelke jnoelke linked an issue Mar 23, 2023 that may be closed by this pull request
Include blood volume fraction and oxygenation in SIMPA output #115
Open
@frisograce frisograce self-assigned this Jun 27, 2024
@frisograce
Merge branch 'refs/heads/develop' into T115_include_bvf
cd9cffa 
# Conflicts:
#	simpa/utils/tissue_properties.py
#	simpa_tests/test_utils/tissue_composition_tests.py
frisograce
frisograce reviewed Jun 28, 2024
View reviewed changes
Copy link
Collaborator

@frisograce frisograce left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Please check how to save bvf in hdf5. It seems not to appear in the output.

simpa/utils/calculate.py Show resolved Hide resolved
simpa/utils/calculate.py Outdated Show resolved Hide resolved
simpa_tests/automatic_tests/tissue_library/test_core_assumptions.py Outdated Show resolved Hide resolved
simpa_tests/automatic_tests/tissue_library/test_core_assumptions.py Outdated
@@ -6,7 +6,9 @@
from simpa.utils import TISSUE_LIBRARY
from simpa.utils.libraries.tissue_library import TissueLibrary
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

remove from simpa.utils.libraries.tissue_library import TissueLibrary

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think without further changes in the code we cannot just remove the import

frisograce and others added 6 commits June 28, 2024 15:07
@frisograce
Merge branch 'develop' into T115_include_bvf
9f8ac78
@jnoelke
apply requested changes and small refactoring
52b5ec0
@jnoelke
Add bvf to simpa output
6af2601 
-  this is achieved by adding it to the wavelength independend properties
@jnoelke
Merge branch 'develop' into T115_include_bvf
6e5e447
@jnoelke
consistent documentation
3066f44
@jnoelke
Refactoring
97519c5 
-  Use a helper function to extract hemoglobin fraction which is used for both sO2 and bvf
-  Remove unnecessary if conditions by using 0.0 as default
- improve type hinting
@jnoelke jnoelke requested a review from frisograce July 26, 2024 18:01
@kdreher kdreher merged commit c0be54b into develop Jul 29, 2024
12 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jgroehl jgroehl jgroehl approved these changes

@frisograce frisograce Awaiting requested review from frisograce

Assignees

@frisograce frisograce

Labels
hacking week
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Include blood volume fraction and oxygenation in SIMPA output
5 participants
@jnoelke @jgroehl @frisograce @kdreher @mschllnbrg