Merge branch 'topic/default/new_fluiddyn' into 'branch/default'

Use fluiddyn 0.6.0

See merge request fluiddyn/fluidimage!70

.hgignore

@@ -77,7 +77,7 @@ image_samples/4th_PIV-Challenge_Case_E/E_Calibration_Images/Camera_0*/calib*.npz
 image_samples/Milestone/Images_many*
 
 image_samples/Karman/Images.civ/*
-image_samples/Karman/Images.*_example*
+image_samples/*/Images.*_example*
 
 .coverage/*
 

CHANGES.md

@@ -3,16 +3,26 @@
 See also the
 [unreleased changes](https://foss.heptapod.net/fluiddyn/fluidimage/-/compare/0.3.0...branch%2Fdefault).
 
-## [0.3.0] (unpublished)
+## [0.3.0] (2024-03-04)
 
-This will be a big breaking release.
+```{warning}
+
+This version contains incompatible API changes documented here.
+
+```
 
 ### Removed
 
-- `strcouple` is replaced by `str_subset`.
+- The parameter `strcouple` is replaced by `str_subset`.
 - `from fluidimage.preproc import PreprocBase` has to be replaced by
   `from fluidimage.preproc import Work`.
 
+### Changed
+
+- Better default for `params.series.str_subset` (`"pairs"` for PIV),
+  `params.series.ind_start` (`"first"`), `params.preproc.series.str_subset` (`"all1by1"`)
+  and `params.preproc.series.ind_first` (`"first"`).
+
 ### Added
 
 - Module {mod}`fluidimage.piv` to import the PIV classes `Work` and `Topology`.

doc/examples/im2im_parallel.py

@@ -22,7 +22,6 @@
 params.args_init = ((1024, 2048), "clip")
 
 params.images.path = "../../image_samples/Jet/Images/c*"
-params.images.str_subset = "60:,:"
 
 params.saving.postfix = "im2im_example"
 params.saving.how = "recompute"

doc/examples/optflow_parallel.py

@@ -4,7 +4,6 @@
 params = Topology.create_default_params()
 
 params.series.path = get_path_image_samples() / "Karman/Images"
-params.series.ind_start = 1
 params.series.ind_step = 2
 
 # params.features._print_doc()

doc/examples/piv_parallel.py

@@ -4,7 +4,6 @@
 params = Topology.create_default_params()
 
 params.series.path = get_path_image_samples() / "Karman/Images"
-params.series.ind_start = 1
 params.series.ind_step = 2
 
 params.piv0.shape_crop_im0 = 32

doc/examples/preproc_parallel.py

@@ -5,7 +5,6 @@
 
 params.preproc.series.path = get_path_image_samples() / "Jet/Images"
 params.preproc.series.str_subset = "i,:"
-params.preproc.series.ind_start = 60
 
 p_tools = params.preproc.tools
 

doc/tutorials/tuto_piv.md

@@ -6,7 +6,7 @@ jupytext:
     format_version: 0.13
     jupytext_version: 1.16.1
 kernelspec:
-  display_name: Python 3
+  display_name: Python 3 (ipykernel)
   language: python
   name: python3
 ---
@@ -29,9 +29,7 @@ path_src = get_path_image_samples() / "Karman/Images"
 postfix = "doc_piv_ipynb"
 ```
 
-```{raw-cell}
-We first import the class :class:`fluidimage.topologies.piv.TopologyPIV`.
-```
+We first import the class {class}`fluidimage.topologies.piv.TopologyPIV`.
 
 ```{code-cell} ipython3
 from fluidimage.piv import Topology
@@ -59,7 +57,6 @@ We can of course modify these parameters. An error will be raised if we accident
 
 ```{code-cell} ipython3
 params.series.path = str(path_src)
-params.series.ind_start = 1
 
 params.piv0.shape_crop_im0 = 64
 params.multipass.number = 2
@@ -69,9 +66,7 @@ params.saving.how = 'recompute'
 params.saving.postfix = postfix
 ```
 
-```{raw-cell}
-In order to run the PIV computation, we have to instanciate an object of the class :class:`fluidimage.topologies.piv.TopologyPIV`.
-```
+In order to run the PIV computation, we have to instanciate an object of the class {class}`fluidimage.topologies.piv.TopologyPIV`.
 
 ```{code-cell} ipython3
 topology = Topology(params)
@@ -153,7 +148,7 @@ with h5py.File("piv_01-02.h5", "r") as file:
 ```
 
 ```{raw-cell}
-Moreover, the final result of this PIV computation can also be manipulated and visualized using :class:`fluidimage.postproc.vector_field.VectorFieldOnGrid`:
+Moreover, the final result of this PIV computation can also be manipulated and visualized using {class}`fluidimage.postproc.vector_field.VectorFieldOnGrid`:
 ```
 
 ```{code-cell} ipython3

pixi.toml

@@ -12,8 +12,8 @@ test = "export OMP_NUM_THREADS=1 && pytest src -v"
 [dependencies]
 python = ">=3.9,<3.11"
 numpy = ">=1.26.3"
-transonic = ">=0.6.1,<0.7"
-fluiddyn = ">=0.5.4,<0.6"
+transonic = ">=0.6.1"
+fluiddyn = ">=0.6.0"
 h5netcdf = ">=1.3.0"
 h5py = ">=3.10.0"
 matplotlib = ">=3.3"

pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
     "h5py",
     "h5netcdf",
     "transonic>=0.6.2",
-    "fluiddyn",
+    "fluiddyn >=0.6.0",
     "pyfftw >= 0.10.4",
     "imageio",
     "scikit-image >= 0.12.3",
@@ -171,3 +171,7 @@ extend-exclude = "/(__pythran__|__python__|__numba__|build|doc/_build|\\.ipynb_c
 profile = "black"
 line_length = 82
 src_paths = ["src", "doc"]
+
+
+[tool.pytest.ini_options]
+addopts = "--pdbcls=IPython.terminal.debugger:TerminalPdb"

src/fluidimage/data_objects/piv.py

@@ -33,35 +33,19 @@
 from .display_piv import DisplayPIV
 
 
-def get_str_index(serie, i, index):
-    if serie._from_movies and i == serie.nb_indices - 1:
-        return str(index)
-
-    if serie._index_types[i] == "digit":
-        code_format = "{:0" + str(serie._index_lens[i]) + "d}"
-        str_index = code_format.format(index)
-    elif serie._index_types[i] == "alpha":
-        if index > 25:
-            raise ValueError('"alpha" index larger than 25.')
-
-        str_index = chr(ord("a") + index)
-    else:
-        raise Exception('The type should be "digit" or "alpha".')
-
-    return str_index
-
-
 def get_name_piv(serie, prefix="piv"):
-    index_slices = serie.get_index_slices()
+    slicing_tuples = serie.get_slicing_tuples()
     str_indices = ""
-    for i, inds in enumerate(index_slices):
+    for idim, inds in enumerate(slicing_tuples):
         index = inds[0]
-        str_index = get_str_index(serie, i, index)
+        str_index = serie.get_str_for_name_from_idim_idx(idim, index)
         if len(inds) > 1:
-            str_index += "-" + get_str_index(serie, i, inds[1] - 1)
+            str_index += "-" + serie.get_str_for_name_from_idim_idx(
+                idim, inds[1] - 1
+            )
 
-        if i > 1:
-            str_indices += serie._index_separators[i - 1]
+        if idim > 1:
+            str_indices += serie.get_index_separators[idim - 1]
         str_indices += str_index
 
     name = prefix + "_" + str_indices + ".h5"
@@ -789,12 +773,12 @@ def _get_name(self, kind):
 
         serie = self.couple.serie
 
-        str_ind0 = serie._compute_strindices_from_indices(
-            *[inds[0] for inds in serie.get_index_slices()]
+        str_ind0 = serie.compute_str_indices_from_indices(
+            *[inds[0] for inds in serie.get_slicing_tuples()]
         )
 
-        str_ind1 = serie._compute_strindices_from_indices(
-            *[inds[1] - 1 for inds in serie.get_index_slices()]
+        str_ind1 = serie.compute_str_indices_from_indices(
+            *[inds[1] - 1 for inds in serie.get_slicing_tuples()]
         )
 
         name = "piv_" + serie.base_name + str_ind0 + "-" + str_ind1 + "_light.h5"