DOC: Blogpost_KD_Week7

posts/2024/2024_07_15_kaustav_week_7.rst

@@ -0,0 +1,113 @@
+My Journey Continues: Week 7 Progress with DIPY
+===============================================
+
+.. post:: July 15 2024
+     :author: Kaustav
+     :tags: google
+     :category: gsoc
+
+Greetings, everyone!
+The seventh week of GSOC has been a fruitful and learning one.
+
+Decorator PR Fixes
+------------------
+
+This week I tried to fix one of the decorator PR(:ref:`PR #3257 <#3257>`). I had implemented a lot of solutions to make the tests pass, but realized I had added unnecessary code, all I had to do was fix the tests.
+Basically I had to add the necessary calls for keyword arguments.
+
+Lazy Loading PR
+---------------
+
+I had submitted a PR for the lazy loading feature last week(:ref:`PR #3288 <#3288>`). I was able to fix most of the problems that I was facing last week, I added a ton of **.pyi** files for various modules.
+I had initiated the review of the PR this week. I hope to get it merged ASAP, maybe in a day or two. Alas this was my biggest learning until now and also quite fun, and I am really thankful for the opportunity to do this work.
+
+Difficulties & Challenges
+-------------------------
+
+While fixing the PRs, these were some of my thoughts
+
+.. _#3257:
+
+1. `PR #3257 <https://github.com/dipy/dipy/pull/3257>`_
+- Most of the issues were fixed thanks to the review by my mentor. One clarification still remains about the **fit_method**. I was receiving error as mentioned below, to fix it it I applied an `else` clause for `fit_method` in `FreeWaterTensorModel`.
+
+.. code-block:: python
+
+    def test_fwdti_singlevoxel():
+        # Simulation when water contamination is added
+        gtf = 0.44444  # ground truth volume fraction
+        mevals = np.array([[0.0017, 0.0003, 0.0003], [0.003, 0.003, 0.003]])
+        S_conta, peaks = multi_tensor(
+            gtab_2s,
+            mevals,
+            S0=100,
+            angles=[(90, 0), (90, 0)],
+            fractions=[(1 - gtf) * 100, gtf * 100],
+            snr=None,
+        )
+        fwdm = fwdti.FreeWaterTensorModel(gtab_2s, "WLS")
+        fwefit = fwdm.fit(S_conta)
+
+    dipy/reconst/tests/test_fwdti.py:100: 
+    _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
+
+    dipy/reconst/multi_voxel.py:40: in new_fit
+        return single_voxel_fit(self, data)
+    dipy/testing/decorators.py:210: in wrapper
+        return convert_positional_to_keyword(func, args, kwargs)
+    dipy/testing/decorators.py:191: in convert_positional_to_keyword
+        return func(*args, **kwargs)
+    _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
+
+    self = <dipy.reconst.fwdti.FreeWaterTensorModel object at 0x13e1ce110>
+    data = array([ 100.        ,   43.50442139,   13.18018944,   33.49286891,
+             18.75861633,   22.62819702,   37.1749802 ,...   5.72778443,
+             29.20758655,    5.17472072,   35.21098605,   27.02812095,
+             20.99614616,    5.7284468 ]), mask = None, kwargs = {}, S0 = 100.0
+
+        @multi_voxel_fit
+        @warning_for_keywords()
+        def fit(self, data, *, mask=None, **kwargs):
+            """Fit method of the free water elimination DTI model class
+        
+            Parameters
+            ----------
+            data : array
+                The measured signal from one voxel.
+            mask : array
+                A boolean array used to mark the coordinates in the data that
+                should be analyzed that has the shape data.shape[:-1]
+            """
+            S0 = np.mean(data[self.gtab.b0s_mask])
+            fwdti_params = self.fit_method(
+                self.design_matrix, data, S0, *self.args, **self.kwargs
+            )
+    E       TypeError: 'str' object is not callable
+
+    dipy/reconst/fwdti.py:161: TypeError
+
+.. _#3254:
+
+2. `PR #3254 <https://github.com/dipy/dipy/pull/3254>`_
+- I am still having issue with this PR, where applying decorator to two specific functions gives me errors. I am assuming the problem arrives because my decorator is not receiving correct signature from the cython function. I was able to resolve it locally through `cython.binding` method but it didn't work out for the CI.
+
+.. _#3288:
+
+3. `PR #3288 <https://github.com/dipy/dipy/pull/3288>`_
+- Very good progress, I have a few little doubts to complete this PR. I will try to ask them in the next meeting session with my mentor. Also for some reason the external libraries are not getting loaded even with correct implementation of `lazy_loader <https://pypi.org/project/lazy-loader/>`__ package. Hopefully I can resolve this soon.
+
+Next Week
+---------
+
+Next week I am planning to take care of some documentation issues that are raised in the repository. Also I have some tasks assigned by my mentor towards improvements of DIPY.
+I have started working on them already, planning to put down the PRs soon.
+
+Final Thoughts
+--------------
+
+The seventh week of the Coding phase has been a progressive one. I learned tons of new stuff and implemented it. Hopefully I can finish the PRs soon and move onto next tasks.
+I am grateful for the guidance and support provided by my mentor `Serge Koudoro <https://github.com/skoudoro>`__, and the DIPY community, which have been instrumental in driving this project forward.
+
+Stay tuned for more updates as I continue to work on enhancing DIPY!
+
+Thank you for reading!