Merge branch 'topic/default/fluidpivviewer' into 'branch/default'

New files for fluidpivviewer

Closes #32

See merge request fluiddyn/fluidimage!85

CHANGES.md

@@ -1,7 +1,15 @@
 # Release notes
 
 See also the
-[unreleased changes](https://foss.heptapod.net/fluiddyn/fluidimage/-/compare/0.4.2...branch%2Fdefault).
+[unreleased changes](https://foss.heptapod.net/fluiddyn/fluidimage/-/compare/0.4.3...branch%2Fdefault).
+
+## [0.4.3] (2024-03-27)
+
+- [!85](https://foss.heptapod.net/fluiddyn/fluidimage/-/merge_requests/85): `fluidpivviewer`.
+- [!84](https://foss.heptapod.net/fluiddyn/fluidimage/-/merge_requests/84): `multi_exec_async`
+  using {class}`fluidimage.topologies.splitters.Splitter`.
+- Other bugfixes and improvements (name PIV files and
+  {class}`fluidimage.postproc.vector_field.VectorFieldOnGrid`).
 
 ## [0.4.2] (2024-03-20)
 
@@ -168,3 +176,4 @@ This version contains incompatible API changes documented here.
 [0.4.0]: https://foss.heptapod.net/fluiddyn/fluidimage/-/compare/0.3.0...0.4.0
 [0.4.1]: https://foss.heptapod.net/fluiddyn/fluidimage/-/compare/0.4.0...0.4.1
 [0.4.2]: https://foss.heptapod.net/fluiddyn/fluidimage/-/compare/0.4.1...0.4.2
+[0.4.3]: https://foss.heptapod.net/fluiddyn/fluidimage/-/compare/0.4.2...0.4.3

doc/conf.py

@@ -13,18 +13,13 @@
 
 import os
 
-os.environ["OMP_NUM_THREADS"] = "1"
-
 import fluidimage
 
-# we want this module to be importable.
-try:
-    import fluidimage.topologies.optical_flow
-except Exception:
-    import traceback
-
-    traceback.print_exc()
+# we want these modules to be importable.
+import fluidimage.topologies.preproc
+import fluidimage.topologies.optical_flow
 
+os.environ["OMP_NUM_THREADS"] = "1"
 # -- General configuration ----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.

doc/examples/piv_parallel.py

@@ -5,11 +5,17 @@
 
 params.series.path = get_path_image_samples() / "Karman/Images"
 
+params.mask.strcrop = "50:350, 0:380"
+
 params.piv0.shape_crop_im0 = 32
-params.multipass.number = 2
-params.multipass.use_tps = False
+params.piv0.displacement_max = 5
+params.piv0.nb_peaks_to_search = 2
 
-params.mask.strcrop = ":, 50:500"
+params.fix.correl_min = 0.4
+params.fix.threshold_diff_neighbour = 2.0
+
+params.multipass.number = 2
+params.multipass.use_tps = "last"
 
 # params.saving.how = 'complete'
 params.saving.postfix = "piv_example"

doc/examples/piv_try_params.py

@@ -4,20 +4,18 @@
 
 params = Work.create_default_params()
 
-params.multipass.number = 2
-params.multipass.use_tps = True
+params.series.path = "../../image_samples/Oseen/Images"
+
+params.mask.strcrop = "30:250, 100:"
 
 params.piv0.shape_crop_im0 = 32
 params.piv0.displacement_max = 5
+
 params.fix.correl_min = 0.2
 params.fix.threshold_diff_neighbour = 8
 
-params.mask.strcrop = "30:250, 100:"
-
-path = "../../image_samples/Oseen/Images"
-# path = '../../image_samples/Karman/Images'
-params.series.path = path
-params.series.str_subset = "i+1:i+3"
+params.multipass.number = 2
+params.multipass.use_tps = True
 
 work = Work(params=params)
 

doc/examples/piv_try_params_Karman.py

@@ -0,0 +1,28 @@
+"""To be run in IPython to find a good set of parameters"""
+
+from fluidimage.piv import Work
+
+params = Work.create_default_params()
+
+params.series.path = "../../image_samples/Karman/Images"
+
+params.mask.strcrop = "50:350, 0:380"
+
+params.fix.correl_min = 0.4
+params.fix.threshold_diff_neighbour = 2.0
+
+params.piv0.shape_crop_im0 = 32
+params.piv0.displacement_max = 5
+params.piv0.nb_peaks_to_search = 2
+
+params.multipass.number = 2
+params.multipass.use_tps = "last"
+
+work = Work(params=params)
+
+piv = work.process_1_serie()
+
+# piv.display(show_interp=True, scale=0.3, show_error=False)
+piv.display(show_interp=False, scale=1, show_error=True)
+
+# piv.save()

doc/tutorials/tuto_piv.md

@@ -66,9 +66,17 @@ the input images:
 path_src = get_path_image_samples() / "Karman/Images"
 params.series.path = str(path_src)
 
-params.piv0.shape_crop_im0 = 64
+params.mask.strcrop = "50:350, 0:400"
+
+params.piv0.shape_crop_im0 = 48
+params.piv0.displacement_max = 5
+params.piv0.nb_peaks_to_search = 2
+
+params.fix.correl_min = 0.4
+params.fix.threshold_diff_neighbour = 2.0
+
 params.multipass.number = 2
-params.multipass.use_tps = False
+params.multipass.use_tps = "last"
 ```
 
 After instantiating the `Work` class,
@@ -204,15 +212,23 @@ params.saving._print_doc()
 path_src = get_path_image_samples() / "Karman/Images"
 params.series.path = str(path_src)
 
-params.piv0.shape_crop_im0 = 64
+params.mask.strcrop = "50:350, 0:400"
+
+params.piv0.shape_crop_im0 = 48
+params.piv0.displacement_max = 5
+params.piv0.nb_peaks_to_search = 2
+
+params.fix.correl_min = 0.4
+params.fix.threshold_diff_neighbour = 2.0
+
 params.multipass.number = 2
-params.multipass.use_tps = False
+params.multipass.use_tps = "last"
 
 params.saving.how = 'recompute'
 params.saving.postfix = "doc_piv_ipynb"
 ```
 
-In order to run the PIV computation, we have to instanciate an object of the class
+In order to run the PIV computation, we have to instantiate an object of the class
 {class}`fluidimage.piv.Topology`.
 
 ```{code-cell} ipython3
@@ -243,6 +259,13 @@ path_src
 topology.path_dir_result
 ```
 
+```{code-cell} ipython3
+sorted(path.name for path in topology.path_dir_result.glob("*"))
+```
+
+Fluidimage provides the command `fluidpivviewer`, which starts a very simple GUI to
+visualize the PIV results.
+
 ## Analyzing the computation
 
 ```{code-cell} ipython3

image_samples/Milestone/piv_0001a-b.h5

@@ -0,0 +1 @@
+./piv_0000a-b.h5

pyproject.toml

@@ -9,7 +9,7 @@ build-backend = 'mesonpy'
 
 [project]
 name = "fluidimage"
-version = "0.4.2"
+version = "0.4.3"
 description = "Fluid image processing with Python."
 authors = [
     {name = "Pierre Augier", email = "[email protected]"},
@@ -55,6 +55,7 @@ Homepage = "https://foss.heptapod.net/fluiddyn/fluidimage"
 fluidimviewer-pg = "fluidimage.gui.pg_main:main"
 fluidimviewer = "fluidimage.gui.imviewer:main"
 fluidimlauncher = "fluidimage.gui.launcher.main:main"
+fluidpivviewer = "fluidimage.gui.piv_viewer:main"
 
 [project.optional-dependencies]
 pims = ["pims"]

src/fluidimage/__init__.py

@@ -65,6 +65,10 @@ def get_path_image_samples():
     if path_image_samples.exists():
         return path_image_samples.resolve()
 
+    path_image_samples = Path.home() / "dev/fluidimage/image_samples"
+    if path_image_samples.exists():
+        return path_image_samples
+
     # Gitlab and Github CI
     for name_env_var_project_dir in ("CI_PROJECT_DIR", "GITHUB_WORKSPACE"):
         ci_project_dir = os.getenv(name_env_var_project_dir)

src/fluidimage/gui/__init__.py

@@ -9,8 +9,10 @@
 .. autosummary::
    :toctree:
 
+   base_matplotlib
    imviewer
    launcher
    pg_main
+   piv_viewer
 
 """

src/fluidimage/gui/base_matplotlib.py

@@ -0,0 +1,32 @@
+"""Base class using matplotlib widgets
+
+"""
+
+from matplotlib.widgets import Button, TextBox
+
+
+class AppMatplotlibWidgets:
+
+    _buttons: dict
+    _textboxes: dict
+
+    def __init__(self):
+        self._buttons = {}
+        self._textboxes = {}
+
+    def _create_button(self, fig, rect, text, func):
+        ax = fig.add_axes(rect)
+        button = Button(ax, text)
+        button.on_clicked(func)
+        self._buttons[text] = button
+        return button
+
+    def _create_text_box(self, fig, rect, name, func, initial):
+        ax = fig.add_axes(rect)
+        textbox = TextBox(ax, name, initial=initial)
+        textbox.on_submit(func)
+        self._textboxes[name] = textbox
+        return textbox
+
+    def get_textbox(self, key):
+        return self._textboxes[key]

src/fluidimage/gui/imviewer.py

@@ -14,11 +14,11 @@
 from glob import glob
 
 import matplotlib.pyplot as plt
-from matplotlib.widgets import Button, TextBox
 
 from fluiddyn.io.image import imread
 from fluiddyn.util import time_as_str
 from fluiddyn.util.serieofarrays import SerieOfArraysFromFiles
+from fluidimage.gui.base_matplotlib import AppMatplotlibWidgets
 from fluidimage.util import safe_eval
 
 extensions = ["png", "tif", "tiff", "jpg", "jpeg", "bmp", "cine"]
@@ -66,7 +66,7 @@ def parse_args():
     return parser.parse_args()
 
 
-class ImageViewer:
+class ImageViewer(AppMatplotlibWidgets):
     """Simple Image viewer."""
 
     def __init__(self, args):
@@ -98,8 +98,7 @@ def __init__(self, args):
         self.nb_images = len(self.path_files)
         print(f"Will use {self.nb_images} images in the dir {path_dir}")
 
-        self._buttons = {}
-        self._textboxes = {}
+        super().__init__()
 
         fig = self.fig = plt.figure()
         fig.canvas.manager.set_window_title(
@@ -133,30 +132,28 @@ def __init__(self, args):
         function_buttons[3] = self._increase_ifile_n
 
         y = size_button / 3.0
-        for i, x in enumerate(x_buttons):
-            name = name_buttons[i]
-            func = function_buttons[i]
+        for x, name, func in zip(x_buttons, name_buttons, function_buttons):
             self._create_button(fig, [x, y, size_button, size_button], name, func)
 
         self._n = 1
 
-        self._create_text(
+        self._create_text_box(
             fig,
             [0.1, y, 2 * size_button, size_button],
             "n = ",
             self._submit_n,
             "1",
         )
 
-        self._create_text(
+        self._create_text_box(
             fig,
             [0.87, 0.92, 1.5 * size_button, size_button],
             "cmax = ",
             self._change_cmax,
             "{:.2f}".format(self.clim[1]),
         )
 
-        self._create_text(
+        self._create_text_box(
             fig,
             [0.87, 0.1, 1.5 * size_button, size_button],
             "cmin = ",
@@ -235,20 +232,6 @@ def change_im(self):
         print("\rchanged to file " + name_file + " " * 20)
         self._image_changing = False
 
-    def _create_button(self, fig, rect, text, func):
-        ax = fig.add_axes(rect)
-        button = Button(ax, text)
-        button.on_clicked(func)
-        self._buttons[text] = button
-        return button
-
-    def _create_text(self, fig, rect, name, func, initial):
-        ax = fig.add_axes(rect)
-        textbox = TextBox(ax, name, initial=initial)
-        textbox.on_submit(func)
-        self._textboxes[name] = textbox
-        return textbox
-
     def _switch(self):
         if self._last_was_increase:
             self._decrease_ifile_n()

src/fluidimage/gui/meson.build

@@ -1,11 +1,14 @@
 
 python_sources = [
   '__init__.py',
+  'base_matplotlib.py',
   'imviewer.py',
   'pg_main.py',
   'pg_wrapper.py',
+  'piv_viewer.py',
   'test_imviewer.py',
   'test_imviewer_pg.py',
+  'test_piv_viewer.py',
 ]
 
 py.install_sources(