Merge pull request #48 from BohndiekLab/main

Merge main updates into develop

.github/workflows/build_wheels.yml

@@ -23,7 +23,7 @@ jobs:
           platforms: all
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.14.1
+        uses: pypa/cibuildwheel@v2.16.5
         env:
           # configure cibuildwheel to build native archs ('auto'), and some
           # emulated ones

.github/workflows/run_tests.yml

@@ -43,7 +43,7 @@ jobs:
         pip install coverage ruff
     - name: Linting
       run: |
-        ruff --format=github --select=E9,F63,F7,F82 --target-version=py37 . # Should do wider tests in the future.
+        ruff --output-format=github --select=E9,F63,F7,F82 --target-version=py37 . # Should do wider tests in the future.
     - name: Run tests
       run: |
         cd tests

README.md

@@ -27,6 +27,10 @@ pip install patato
 
 To setup support for image reconstruction on Windows, or for GPU support, please follow the installation guide in the documentation.
 
+## Citing PATATO
+
+To cite PATATO, please reference our article in the Journal of Open Source software, [here](https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7). 
+
 ## Documentation, examples and contributing
 Documentation for PATATO can be found at https://patato.readthedocs.io/en/latest/?badge=latest.
 

docs/api/analysis_code.rst

@@ -1,5 +1,5 @@
-MSOT Analysis Code
-===================
+PATATO API Reference
+=====================
 
 .. autosummary::
    :toctree: ../_autosummary

docs/index.rst

@@ -41,6 +41,11 @@ for the community as we translate photoacoustics to the clinic.
 
 The logo was designed by `Elly Pugh <https://ellypugh.com/>`_.
 
+Cite PATATO
+"""""""""""""""
+
+To cite PATATO, please reference our Journal of Open Source Software paper `here <https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7>`_. 
+
 .. only:: latex
 
     User Guide

docs/intro/04_runningtests.rst

@@ -8,7 +8,10 @@ run the following in the command line:
 
     git clone https://github.com/BohndiekLab/patato
     cd patato
-    pip install -e .
+
+Install PATATO: `pip install -e .` (requires build tools) OR `pip install patato` (doesn't require compiler tools).
+
+.. code-block:: console
     cd tests
     python -m unittest
 

paper/paper.md

@@ -14,18 +14,21 @@ authors:
     orcid: 0000-0002-2652-4190
     affiliation: "1, 2" # (Multiple affiliations must be quoted)
   - name: Janek Gröhl
+    orcid: 0000-0002-5332-4856
     affiliation: "1, 2"
   - name: Lina Hacker
+    orcid: 0000-0001-5160-0952
     affiliation: "1, 2, 3"
   - name: Sarah E. Bohndiek
+    orcid: 0000-0003-0371-8635
     corresponding: true # (This is how to denote the corresponding author)
     affiliation: "1, 2"
 affiliations:
-  - name:  CRUK Cambridge Institute, University of Cambridge, UK
+  - name:  CRUK Cambridge Institute, University of Cambridge, United Kingdom
     index: 1
-  - name: Department of Physics, University of Cambridge, UK
+  - name: Department of Physics, University of Cambridge, United Kingdom
     index: 2
-  - name: Department of Oncology, University of Oxford, UK
+  - name: Department of Oncology, University of Oxford, United Kingdom
     index: 3
 date: 8 June 2023
 bibliography: bibliography.bib

patato/io/msot_data.py

@@ -374,7 +374,7 @@ def get_responding_pixels(self, nsigma=2):
             responding = delta_images.raw_data > nsigma * sigma_so2.raw_data
         else:
             return None
-        return SingleImage(responding, None, algorithm_id=delta_images.algorithm_id,
+        return SingleImage(responding, ["Responding Pixels"], algorithm_id=delta_images.algorithm_id,
                            attributes=delta_images.attributes,
                            hdf5_sub_name=delta_images.hdf5_sub_name, field_of_view=delta_images.fov_3d)
 
@@ -697,7 +697,8 @@ def dataset(self):
         return self.get_time_series()
 
     def summary_measurements(self, metrics=None,
-                             include_rois=None, roi_kwargs=None, just_summary=True, return_masks=False):
+                             include_rois=None, roi_kwargs=None, just_summary=True, 
+                             return_masks=False, metric_limits=None):
         """
 
         Parameters
@@ -760,6 +761,10 @@ def summary_measurements(self, metrics=None,
                 if m:
                     mask, data_slice = roi.to_mask_slice(m)
                     output_roi[metrics[i]] = data_slice.raw_data.T[mask.T].T
+                    if metric_limits is not None and metrics[i] in metric_limits:
+                        lower, upper = metric_limits[metrics[i]]
+                        output_roi[metrics[i]][output_roi[metrics[i]] < lower] = np.nan
+                        output_roi[metrics[i]][output_roi[metrics[i]] > upper] = np.nan
                 else:
                     print(f"Skipping metric {metrics[i]}")
 
@@ -778,9 +783,9 @@ def summary_measurements(self, metrics=None,
 
         output_table = pd.DataFrame(outputs)
 
-        summary_methods = {"mean": np.mean,
-                           "median": np.median,
-                           "std": np.std}
+        summary_methods = {"mean": np.nanmean,
+                           "median": np.nanmedian,
+                           "std": np.nanstd}
         for name, method in summary_methods.items():
             for metric in metrics:
                 if metric in output_table.columns:

pyproject.toml

@@ -9,7 +9,7 @@ dependencies = [
     "requests",
     "cython",
     "shapely",
-    "pylops >= 2", # Check version compatibility with pylops
+    "pylops == 2.1", # Check version compatibility with pylops
     "h5py",
     "typing_extensions",
     "pandas",