DCE-dro by MohamedNasser8 · Pull Request #39 · OSIPI/osipy

MohamedNasser8 · 2024-07-18T16:18:06Z

PR: Updates to DRO Code

I have made some updates to the DRO code, based on the existing code from TF6.

Changes Made:

Removed Extra Code for Reading Functions:
- The original code included separate functions for reading slices, 4D data, and DICOM files. I streamlined this by removing the extra reading functions.
- I replaced these with a single function read_dicoms_as_4d_signal which takes a path and returns a 4D MR dataset.
Added Animation Functionality:
- The existing animation function wasn't working properly, so I updated it.
- The new function allows for displaying animations of different slices or the same slice animated over time.
Removed Directory Creation and Data Saving Code:
- I removed the code responsible for creating directories and saving data for now, to simplify the codebase.
Additions
- I implemented Tofts and Extended Tofts models using a parallel approach as their fitting function is time-consuming.
- Used OSIPI methods to calculate the concentration of the tissue after fitting.

Added fitting for 1 voxel and for the whole image

LucyKershaw

I think the issue with this code is that it still rewrites some of the existing osipi functions instead of using them directly, e.g. osipi.S_to_C_via_R1_SPGR

There is a lot of good work here, I'm keen to see the documentation

MohamedNasser8 · 2024-08-27T19:55:28Z

@LucyKershaw Yeah, initially I was copying the code as is without modifying the functions, but I'll update it to rely on the osipi functions. There were a lot of questions and some lines that were unclear to me, which is why I didn't change them earlier.

ltorres6 · 2024-09-04T01:48:21Z

@MohamedNasser8 Can you update this branch to use existing functions to remove redundancy?

ltorres6 · 2024-09-04T02:21:45Z

src/osipi/DRO/main.py

+    # trans_K1 = mf_K1.copy()
+    # trans_k2 = mf_k2.copy()
+    # trans_Vp = mf_Vp.copy()
+    #
+    # vmax_K1, vmax_k2, vmax_Vp = 1, 1, 0.2
+    # vmin_K1, vmin_k2, vmin_Vp = 0.2, 0.2, 0.01
+    # lb_K1, lb_k2, lb_Vp = 0.54, 0.52, 0.49
+    # ub_K1, ub_k2, ub_Vp = 1.52, 1.5, 1.43
+    # lim_K1, lim_k2, lim_Vp = vmax_K1 + 0.5, vmax_k2 + 0.1, vmax_Vp + 0.5
+    # ub_lim = 1.01
+    #
+    # trans_K1[trans_K1 <= vmin_K1] = trans_K1[trans_K1 <= vmin_K1] * lb_K1
+    # trans_K1[trans_K1 >= lim_K1] = trans_K1[trans_K1 >= lim_K1] * ub_lim
+    # trans_K1[(trans_K1 >= vmax_K1) & (trans_K1 < lim_K1)] = (
+    #     trans_K1[(trans_K1 >= vmax_K1) & (trans_K1 < lim_K1)] * ub_K1
+    # )
+    # trans_K1[(trans_K1 > vmin_K1) & (trans_K1 < vmax_K1)] = trans_K1[
+    #     (trans_K1 > vmin_K1) & (trans_K1 < vmax_K1)
+    # ] * (
+    #     lb_K1
+    #     + (
+    #         (
+    #             (trans_K1[(trans_K1 > vmin_K1) & (trans_K1 < vmax_K1)] - vmin_K1)
+    #             / (vmax_K1 - vmin_K1)
+    #         )
+    #         * (ub_K1 - lb_K1)
+    #     )
+    # )
+    #
+    # trans_k2[trans_k2 <= vmin_k2] = trans_k2[trans_k2 <= vmin_k2] * lb_k2
+    # trans_k2[trans_k2 >= lim_k2] = trans_k2[trans_k2 >= lim_k2] * ub_lim
+    # trans_k2[(trans_k2 >= vmax_k2) & (trans_k2 < lim_k2)] = (
+    #     trans_k2[(trans_k2 >= vmax_k2) & (trans_k2 < lim_k2)] * ub_k2
+    # )
+    # trans_k2[(trans_k2 > vmin_k2) & (trans_k2 < vmax_k2)] = trans_k2[
+    #     (trans_k2 > vmin_k2) & (trans_k2 < vmax_k2)
+    # ] * (
+    #     lb_k2
+    #     + (
+    #         (
+    #             (trans_k2[(trans_k2 > vmin_k2) & (trans_k2 < vmax_k2)] - vmin_k2)
+    #             / (vmax_k2 - vmin_k2)
+    #         )
+    #         * (ub_k2 - lb_k2)
+    #     )
+    # )
+    #
+    # trans_Vp[trans_Vp <= vmin_Vp] = trans_Vp[trans_Vp <= vmin_Vp] * lb_Vp
+    # trans_Vp[(trans_Vp >= lim_Vp)] = trans_Vp[trans_Vp >= lim_Vp] * ub_lim
+    # trans_Vp[(trans_Vp >= vmax_Vp) & (trans_Vp < lim_Vp)] = (
+    #     trans_Vp[(trans_Vp >= vmax_Vp) & (trans_Vp < lim_Vp)] * ub_Vp
+    # )
+    # trans_Vp[(trans_Vp > vmin_Vp) & (trans_Vp < vmax_Vp)] = trans_Vp[
+    #     (trans_Vp > vmin_Vp) & (trans_Vp < vmax_Vp)
+    # ] * (
+    #     lb_Vp
+    #     + (
+    #         (
+    #             (trans_Vp[(trans_Vp > vmin_Vp) & (trans_Vp < vmax_Vp)] - vmin_Vp)
+    #             / (vmax_Vp - vmin_Vp)
+    #         )
+    #         * (ub_Vp - lb_Vp)
+    #     )
+    # )
+    #
+    # trans_Vp[trans_Vp > 1] = 1
+    #
+    # Ctiss_tr = forward_extended_tofts(trans_K1, trans_k2, trans_Vp, Ea, t)
+    #
+    # R1_tr, R2st_tr = calcR1_R2(R10, R20st_value, r1, r2st, Ctiss_tr)
+    # dro_S_tr, M_tr = Conc2Sig_Linear(Tr, Te, fa, R1_tr, R2st_tr, signal[:, :, :8, :], 1, M)
+    #
+    # dro_Snoise_tr = addnoise(1, stdS, dro_S_tr, Nt=data_shape[-1])
+    #
+    # animate_mri(signal, mode="time", slice_index=7, time_index=5)
+    # animate_mri(dro_Snoise_tr, mode="time", slice_index=7, time_index=5)
+    # animate_mri(dro_Snoise, mode="time", slice_index=7, time_index=5)


We can remove.

ltorres6 · 2024-09-04T02:26:15Z

In addition to what Lucy mentioned above:

Please use snake_case for each of the functions and CamelCase for the classes.
These functions need unit tests. We will discuss code coverage in our next meeting. This will be an additional hook, and we will set code coverage to 95% of code.
The display functions should go under a utilities module. Now is a good time to create the osipi.utils module.

- add imports as osipi dro - refactor function name to be snake case - added save function in utils

Begin DRO basic functions

c79ff0c

MohamedNasser8 changed the title ~~Dce dro~~ DCE-dro Jul 18, 2024

MohamedNasser8 requested a review from ltorres6 July 18, 2024 23:20

MohamedNasser8 added 7 commits July 19, 2024 21:45

Create signal to concentration methods

d653e40

Create forward tofts function

eb9b39f

display slices and select specific region

24afe12

All pipeline of DRO is finished

327c892

Create ETM nonlinear fitting

331b23a

create ETM non_linear fitting

41f55cd

Added fitting for 1 voxel and for the whole image

finished full pipeline using different models

47131c9

ltorres6 changed the base branch from main to docs August 5, 2024 14:56

ltorres6 changed the base branch from docs to main August 8, 2024 14:56

Illustrate dro code steps, use osipi models for the fitting

d9c2f99

LucyKershaw reviewed Aug 26, 2024

View reviewed changes

ltorres6 reviewed Sep 4, 2024

View reviewed changes

MohamedNasser8 added 3 commits September 5, 2024 01:54

name refactoring, add imports

b054379

- add imports as osipi dro - refactor function name to be snake case - added save function in utils

Add save dicoms function

4df8bcd

solving save function bug

9b7a275

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DCE-dro#39

DCE-dro#39
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MohamedNasser8 commented Jul 18, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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PR: Updates to DRO Code

Changes Made:

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