Fix the documentation

CHANGES.md

@@ -3,6 +3,23 @@
 See also the
 [unreleased changes](https://foss.heptapod.net/fluiddyn/fluidimage/-/compare/0.2.0...branch%2Fdefault).
 
+## [0.3.9] (unpublished)
+
+This will be a big breaking release.
+
+### Removed
+
+- `strcouple` is replaced by `str_subset`.
+- `from fluidimage.preproc import PreprocBase` has to be replaced by
+  `from fluidimage.preproc import Work`.
+
+### Added
+
+- Module {mod}`fluidimage.piv` to import the PIV class `Work` and `Topology`.
+- The work classes {class}`fluidimage.piv.Work` and {class}`fluidimage.preproc.Work`
+  now have parameters in `params.series` and a method
+  {func}`fluidimage.work.BaseWorkFromSerie.process_1_serie`.
+
 ## [0.2.0] (2024-02-19)
 
 - Python >=3.9,<3.12

doc/conf.py

@@ -104,6 +104,7 @@
     "**.ipynb_checkpoints",
     "_jupyter_cache",
     "ipynbslides",
+    "**/.pytest_cache",
 ]
 
 # The reST default role (used for this markup: `text`) to use for all
@@ -139,7 +140,7 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-# html_theme_options = {}
+html_theme_options = {"navigation_with_keys": False}
 
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []

doc/examples/piv_cluster.md

@@ -6,7 +6,7 @@ cluster. We need a script for the computation and a script to submit the job.
 We call the script for the computation `piv_complete.py`. For idempotent job,
 it is important to set `params.saving.how = 'complete'`.
 
-```{literalinclude} piv_complete.py
+```{literalinclude} piv_with_topo_complete.py
 ```
 
 The submission script is quite simple:

doc/examples/preproc.md

@@ -23,7 +23,7 @@ standard preprocessing to images.
 ### Preprocessing one serie
 
 To find the good parameter, you can use the class
-{class}`fluidimage.preproc.base.PreprocBase` (see also
+{class}`fluidimage.work.preproc.Work` (see also
 {mod}`fluidimage.preproc`).
 
 ```{literalinclude} preproc_try_params.py

doc/examples/preproc_with_topology.py

@@ -1,10 +1,11 @@
 from fluidimage import get_path_image_samples
-from fluidimage.topologies.preproc import TopologyPreproc
+from fluidimage.preproc import Topology
 
-params = TopologyPreproc.create_default_params()
+params = Topology.create_default_params()
 
 params.preproc.series.path = get_path_image_samples() / "Jet/Images"
-params.preproc.series.str_subset = "i+60:i+62, 0"
+params.preproc.series.str_subset = "i,:"
+params.preproc.series.ind_start = 60
 
 print("Available preprocessing tools: ", params.preproc.tools.available_tools)
 params.preproc.tools.sequence = [
@@ -25,7 +26,7 @@
 params.preproc.tools.global_threshold.enable = True
 params.preproc.tools.global_threshold.minima = 0.0
 
-topology = TopologyPreproc(params, logging_level="info")
+topology = Topology(params, logging_level="info", nb_max_workers=4)
 
 # Compute in parallel
 topology.compute()

src/fluidimage/preproc/__init__.py

@@ -11,7 +11,9 @@
    :toctree:
 
    toolbox
-   image2image
+   _toolbox_cv
+   _toolbox_py
+   io
 
 """
 

src/fluidimage/preproc/_toolbox_cv.py

@@ -1,9 +1,10 @@
-"""Preprocess toolbox (:mod:`fluidimage.pre_proc._toolbox_cv`)
-==============================================================
+"""Preprocess toolbox
+=====================
+
 A toolbox for preprocessing images. Based on OpenCV library.
 cf. http://www.opencv.org.cn/opencvdoc/2.3.2/html/modules/imgproc/doc/filtering.html
 
-.. currentmodule:: fluidimage.pre_proc._toolbox_cv
+.. currentmodule:: fluidimage.preproc._toolbox_cv
 
 Provides:
 

src/fluidimage/preproc/_toolbox_py.py

@@ -1,5 +1,6 @@
-"""Preprocess toolbox (:mod:`fluidimage.preproc._toolbox_py`)
-==========================================================
+"""Preprocess toolbox
+=====================
+
 A toolbox for preprocessing images.
 Utilizes functions available from `scipy.ndimage` and `skimage` packages.
 cf. http://www.scipy-lectures.org/advanced/image_processing/

src/fluidimage/preproc/io.py

@@ -1,5 +1,5 @@
-"""Handles I/O of images to tools(:mod:`fluidimage.preproc.io`)
-===============================================================
+"""Handles I/O of images to tools
+=================================
 
 Provides decorators to handle input and output of images for tools/functions in
 :mod:`fluidimage.preproc.toolbox`.

src/fluidimage/preproc/toolbox.py

@@ -1,5 +1,5 @@
-"""Preprocess toolbox (:mod:`fluidimage.preproc.toolbox`)
-=========================================================
+"""Preprocess toolbox
+=====================
 
 A toolbox of filters which operate on a single image (numpy array).
 cf. http://www.scipy-lectures.org/advanced/image_processing/

src/fluidimage/topologies/base.py

@@ -118,12 +118,14 @@ class TopologyBase:
 
     """
 
+    _short_name = "base"
+
     @classmethod
     def _add_default_params_saving(cls, params):
 
         params._set_child(
             "saving",
-            attribs={"path": None, "how": "ask", "postfix": "piv"},
+            attribs={"path": None, "how": "ask", "postfix": cls._short_name},
             doc="""Saving of the results.
 
 path : None or str

src/fluidimage/topologies/bos.py

@@ -54,6 +54,8 @@ class TopologyBOS(TopologyBase):
 
     """
 
+    _short_name = "bos"
+
     @classmethod
     def create_default_params(cls):
         """Class method returning the default parameters.
@@ -102,7 +104,7 @@ def create_default_params(cls):
 """
         )
 
-        TopologyBase._add_default_params_saving(params)
+        super()._add_default_params_saving(params)
         params.saving.postfix = "bos"
 
         WorkPIV._complete_params_with_default(params)

src/fluidimage/topologies/example.py

@@ -79,6 +79,8 @@ class TopologyExample(TopologyBase):
 
     """
 
+    _short_name = "example"
+
     @classmethod
     def create_default_params(cls):
         params = dict(

src/fluidimage/topologies/image2image.py

@@ -51,6 +51,8 @@ class TopologyImage2Image(TopologyBase):
 
     """
 
+    _short_name = "im2im"
+
     @classmethod
     def create_default_params(cls):
         """Class method returning the default parameters.

src/fluidimage/topologies/optical_flow.py

@@ -18,6 +18,7 @@ class TopologyOpticalFlow(TopologyPIV):
     """Optical flow topology (Lukas Kanade method)"""
 
     WorkVelocimetry = WorkOpticalFlow
+    _short_name = "optflow"
 
     @classmethod
     def create_default_params(cls):
@@ -34,7 +35,6 @@ def create_default_params(cls):
         """
 
         params = super().create_default_params()
-        params.saving.postfix = "optflow"
         return params
 
 

src/fluidimage/topologies/piv.py

@@ -47,6 +47,8 @@ class TopologyPIV(TopologyBase):
 
     """
 
+    _short_name = "piv"
+
     WorkVelocimetry = WorkPIV
 
     @classmethod
@@ -64,7 +66,7 @@ def create_default_params(cls):
         """
         params = ParamContainer(tag="params")
 
-        TopologyBase._add_default_params_saving(params)
+        super()._add_default_params_saving(params)
 
         cls.WorkVelocimetry._complete_params_with_default(params)
 

src/fluidimage/topologies/preproc.py

@@ -56,6 +56,8 @@ class TopologyPreproc(TopologyBase):
 
     """
 
+    _short_name = "pre"
+
     @classmethod
     def create_default_params(cls, backend="python"):
         """Class method returning the default parameters.
@@ -120,7 +122,7 @@ def create_default_params(cls, backend="python"):
 """
         )
 
-        TopologyBase._add_default_params_saving(params.preproc)
+        super()._add_default_params_saving(params.preproc)
 
         params.preproc.saving._set_attribs(
             {
@@ -332,6 +334,9 @@ def fill_subsets_of_names_and_paths(
             for name, path in subset.get_name_path_arrays():
                 queue_paths[name] = path
 
+        print(f"{queue_subsets_of_names = }")
+        print(f"{queue_paths}")
+
     def make_subsets(self, input_queues: Tuple[Dict], output_queue: Dict) -> bool:
         """Create the subsets of images"""
         queue_subsets_of_names, queue_arrays = input_queues

src/fluidimage/topologies/surface_tracking.py

@@ -52,6 +52,8 @@ class TopologySurfaceTracking(TopologyBase):
 
     """
 
+    _short_name = "surf"
+
     @classmethod
     def create_default_params(cls):
         """Class method returning the default parameters."""
@@ -99,7 +101,7 @@ def create_default_params(cls):
 """
         )
 
-        TopologyBase._add_default_params_saving(params)
+        super()._add_default_params_saving(params)
 
         params._set_internal_attr(
             "_value_text",