Merge branch 'release' into 'master'

Release alpha 1.6.2a1 See merge request 3d/PandoraBox/pandora!367
CNES · Sep 9, 2024 · 06c1c23 · 06c1c23
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diff --git a/AUTHORS.md b/AUTHORS.md
@@ -30,6 +30,7 @@ This file keeps track of authors contributions.
 * Mathis Roux <[email protected]>
 * David Youssefi <[email protected]>
 * Roman Malinowski <[email protected]>
+* Tommy Calendini <[email protected]>
 
 Update here with new contributors.
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,25 @@
 # Changelog
 
+## 1.6.2a1 (September 2024)
+
+### Added
+- Using the numba cache. [#413]
+- Modification of check_conf to compare the disparity interval with the image size. [#411]
+- Addition of a spline order parameter to the shift_right_img method. [#420]
+- Add possibility to not use numba cache. [#421]
+
+### Changed
+- Update criteria documentation. [#410]
+- Changing the after callback to before in the state machine. [#407]
+- Updating the filtering.rst, a documentation file. [#414]
+- Remove numpy warning. [#408]
+
+### Fixed
+- Solving problems displaying images in notebooks. [#409]
+- Move the _indicator parameter to remove the sphinx warning. [#416]
+- Risk normalisation by external global interval. [#418]
+- Use of ‘max’ measurement type with ambiguity. [#404]
+
 ## 1.6.1 (June 2024)
 
 ### Changed

diff --git a/docs/source/exploring_the_field/criteria.rst b/docs/source/exploring_the_field/criteria.rst
@@ -70,7 +70,7 @@ criteria is raised and 0 otherwise.
      - Information
      - pixel interval regularized
 
-These criteria are stored in a xarray `validity_mask` in cost volume et disparity map datasets. 
+These criteria are stored in a Xarray.DataArray `validity_mask` in cost volume and disparity map Xarray.Datasets.
 The `validity_mask` is the same size as the left image.  
 
 Criteria can be linked to user configuration, disparity range, or mismatch and occlusion for instance. 
@@ -148,7 +148,7 @@ is invalid when it contains no data points or when it is outside the image.
 
 Criteria 1 is also set after the cost volume computation for points that meet two conditions: 
 
-- their cost volume is equal to nan for all disparities in the disparity range.
+- their cost volume are NaN for all disparities in the disparity range.
 - they are not on the edge of the image. 
 
 **Criteria 2: right incomplete disparity range**
@@ -212,8 +212,8 @@ For the example with `window_size=3`, `disparity_range=[-2, 2]`, `offset=1` and
 
 .. image:: ../Images/validity_mask_before_cv.drawio.png
 
-As explained before, the validity_mask is also updated after the cost volume computation : we add criteria 1 for points which have 
-cost volume equals to nan for all disparities and which are not on the border. 
+As explained before, the validity_mask is also updated after the cost volume computation : we add criteria 1 for points which are NaN in the
+cost volume for all disparities and which are not on the border.
 Then, at the end of the matching cost step we obtain the following validity mask: 
 
 .. image:: ../Images/validity_mask_matching_cost.drawio.png
@@ -230,7 +230,7 @@ Criteria 3 is raised when the subpixel interpolation does not succeed for a poin
 Validity mask after refinement step
 -----------------------------------
 
-In our previous example, after a refinement step with a quadratic method with obtain the following validity mask: 
+In our previous example, after a refinement step with a quadratic method we obtain the following validity mask:
 
 .. image:: ../Images/validity_mask_refinement.drawio.png
 

diff --git a/docs/source/userguide/faq.rst b/docs/source/userguide/faq.rst
@@ -125,4 +125,10 @@ How can I disable numba parallelization?
 ****************************************
 
 Some functions of Pandora are parallelized using the numba package. To prevent the use of this tool, it is possible to set
-an environment variable named **PANDORA_NUMBA_PARALLEL** to **false**.
+an environment variable named **PANDORA_NUMBA_PARALLEL** to **false**.
+
+How can I disable numba cache?
+******************************
+
+Some Pandora functions have a cache of the numba package. This cache can improve execution speed. To do this, you can set
+an environment variable named **PANDORA_NUMBA_PAR** to **true**.
diff --git a/docs/source/userguide/step_by_step/filtering.rst b/docs/source/userguide/step_by_step/filtering.rst
@@ -14,91 +14,149 @@ The filtering methods allow to homogenize the disparity maps, those available in
 
 .. note::  Invalid pixels are not filtered. If a valid pixel contains an invalid pixel in its filter, the invalid pixel is ignored for the calculation
 
+**Configuration and parameters**
 
-.. list-table:: Configuration and parameters
-   :widths: 19 19 19 19 19 19
-   :header-rows: 1
-
-
-   * - Name
-     - Description
-     - Type
-     - Default value
-     - Available value
-     - Required
-   * - *filter_method*
-     - Filtering method
-     - str
-     -
-     - | "median",
-       | "bilateral",
-       | "median_for_intervals"
-     - Yes
-   * - *filter_size*
-     - Filter's size
-     - int
-     - 3
-     - >=1
-     - No. Only available if "median" or "median_for_intervals" filter
-   * - *sigma_color*
-     - Bilateral filter parameter
-     - float
-     - 2.0
-     - 
-     - No. Only available if "bilateral" filter
-   * - *sigma_space*
-     - Bilateral filter parameter
-     - float
-     - 6.0
-     - 
-     - No. Only available if "bilateral" filter
-   * - *interval_indicator*
-     - | Indicator for which interval to filter.
-       | Ex: If *cfg* contains a step "cost_volume_confidence.intervals"
-       | then *interval_indicator* should be "intervals"
-     - str
-     - ""
-     - 
-     - No. Only available if "median_for_intervals" filter
-   * - *regularization*
-     - Activate regularization
-     - bool
-     - false
-     - true, false
-     - No. Only available if "median_for_intervals" filter
-   * - *ambiguity_indicator*
-     - | Indicator for which ambiguity to use during regularization.
-       | Ex: If *cfg* contains a step "cost_volume_confidence.amb"
-       | then *ambiguity_indicator* should be "amb"
-     - str
-     - ""
-     - 
-     - No. Only available if "median_for_intervals" filter
-   * - *ambiguity_threshold*
-     - A pixel is regularized if threshold>ambiguity
-     - float
-     - 0.6
-     - >0 and <1
-     - No. Only available if "median_for_intervals" filter
-   * - *ambiguity_kernel_size*
-     - Ambiguity kernel size for regularization. See publication for details.
-     - int
-     - 5
-     - >=0
-     - No. Only available if "median_for_intervals" filter
-   * - *vertical_depth*
-     - Depth for graph regularization. See publication for details.
-     - int
-     - 2
-     - >=0
-     - No. Only available if "median_for_intervals" filter
-   * - *quantile_regularization*
-     - Quantile used for regularization
-     - float
-     - 0.9
-     - >=0 and <=1
-     - No. Only available if "median_for_intervals" filter
+.. tabs:: 
 
+    .. tab:: Median
+
+        .. tabs:: 
+
+            .. list-table:: 
+                :widths: 19 19 19 19 19 19
+                :header-rows: 1
+
+                * - Name
+                  - Description
+                  - Type
+                  - Default value
+                  - Available value
+                  - Required
+                * - filter_method
+                  - Filtering method
+                  - str
+                  - 
+                  - "median"
+                  - Yes
+                * - filter_size
+                  - Filter's size
+                  - int
+                  - 3
+                  - >=1
+                  - No
+
+    .. tab:: Bilateral
+
+        .. tabs:: 
+
+            .. list-table:: 
+                :widths: 19 19 19 19 19 19
+                :header-rows: 1
+
+                * - Name
+                  - Description
+                  - Type
+                  - Default value
+                  - Available value
+                  - Required
+                * - filter_method
+                  - Filtering method
+                  - str
+                  - 
+                  - "bilateral"
+                  - Yes
+                * - sigma_color
+                  - Bilateral filter parameter
+                  - float
+                  - 2.0
+                  - 
+                  - No
+                * - sigma_space
+                  - Bilateral filter parameter
+                  - float
+                  - 6.0
+                  - 
+                  - No
+
+    .. tab:: Median for intervals
+
+        .. tabs:: 
+
+            .. list-table:: 
+                :widths: 19 19 19 19 19 19
+                :header-rows: 1
+
+                * - Name
+                  - Description
+                  - Type
+                  - Default value
+                  - Available value
+                  - Required
+                * - filter_method
+                  - Filtering method
+                  - str
+                  - 
+                  - "median_for_intervals"
+                  - Yes
+                * - filter_size
+                  - Filter’s size
+                  - int
+                  - 3
+                  - >=1
+                  - No
+                * - interval_indicator
+                  - | Indicator for which interval to filter.
+                    |
+                    | Ex: If cfg contains a step
+                    | “cost_volume_confidence.intervals” then
+                    | interval_indicator should be “intervals”
+                  - str
+                  - ""
+                  - 
+                  - No
+                * - regularization
+                  - Activate regularization
+                  - bool
+                  - False
+                  - True, False
+                  - No
+                * - ambiguity_indicator
+                  - | Indicator for which ambiguity to use during
+                    | regularization.
+                    |
+                    | Ex: If cfg contains a step
+                    | “cost_volume_confidence.amb” then
+                    | ambiguity_indicator should be “amb”
+                  - str
+                  - ""
+                  - 
+                  - No
+                * - ambiguity_threshold
+                  - A pixel is regularized if threshold>ambiguity
+                  - float
+                  - 0.6
+                  - >0 and <1
+                  - No
+                * - ambiguity_kernel_size
+                  - | Ambiguity kernel size for regularization.
+                    | See publication for details.
+                  - int
+                  - 5
+                  - >=0
+                  - No
+                * - vertical_depth
+                  - | Depth for graph regularization.
+                    | See publication for details.
+                  - int
+                  - 2
+                  - >=0 
+                  - No
+                * - quantile_regularization
+                  - Quantile used for regularization
+                  - float
+                  - 0.9
+                  - >=0 and <=1
+                  - No        
 
 **Example**
 

diff --git a/notebooks/introduction_and_basic_usage.ipynb b/notebooks/introduction_and_basic_usage.ipynb
@@ -543,10 +543,12 @@
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "<img src=\"../docs/source/Images/Machine_state_diagram.png\" width=\"700\">"
+    "Image(\"../docs/source/Images/Machine_state_diagram.png\")"
    ]
   },
   {

diff --git a/notebooks/usage_with_multiscale.ipynb b/notebooks/usage_with_multiscale.ipynb
@@ -572,10 +572,12 @@
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "<img src=\"../docs/source/Images/Machine_state_diagram.png\" width=\"700\">"
+    "Image(\"../docs/source/Images/Machine_state_diagram.png\")"
    ]
   },
   {