Merge remote-tracking branch 'origin/main' into update_conda_versions

.env/conda/enmapbox_full_3.38.yml

@@ -17,7 +17,7 @@ dependencies:
 - flake8
 - git-lfs
 - gitpython
-- hy5py
+- h5py
 - lightgbm
 - matplotlib
 - netcdf4

.env/conda/enmapbox_full_latest.yml

@@ -17,7 +17,7 @@ dependencies:
 - flake8
 - git-lfs
 - gitpython
-- hy5py
+- h5py
 - lightgbm
 - matplotlib
 - netcdf4

.env/conda/enmapbox_full_longterm.yml

@@ -17,7 +17,7 @@ dependencies:
 - flake8
 - git-lfs
 - gitpython
-- hy5py
+- h5py
 - lightgbm
 - matplotlib
 - netcdf4

.flake8

@@ -59,7 +59,7 @@ per-file-ignores =
     #  QGS104 Use 'import qgis.PyQt.pyrcc_main' instead of 'import PyQt5.pyrcc_main'
     # just not available in OSGeo4W installations
     # script should run immediately which site.addsitedir(REPO) before other imports
-    scripts/*.py : E402
+    # scripts/*.py : E402
     enmapbox/eo4qapps/geetimeseriesexplorerapp/*.py : F821
     enmapbox/__main__.py: E402
     enmapbox/gui/__init__.py: F401

.github/workflows/flake8.yml

@@ -19,7 +19,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.12"
       - name: Run flake8
         uses: julianwachholz/flake8-action@v2
         with:

.github/workflows/run-tests-mamba.yml

@@ -3,7 +3,7 @@ name: 🐍 Conda Environments
 on:
   push:
     branches:
-      - mamba**
+      - main
       - release-**
 
   pull_request:

.github/workflows/urlcheck.yml

@@ -4,12 +4,12 @@ on:
   push:
     branches:
       - main
-      - 'releases/**'
+      - 'release_**'
       - urlcheck
   pull_request:
     branches:
       - main
-      - 'releases/**'
+      - 'release_**'
 
 jobs:
   build:
@@ -34,7 +34,7 @@ jobs:
         force_pass : false
 
         exclude_files:
-          test_glossary.py,snippets/grabPotsdamWmsData.py
+          test_glossary.py,snippets/grabPotsdamWmsData.py,scripts/update_splashscreen.py
 
         # {z}/{x}/{y}: ESRI
         # {z]/{y}/{x}: CartoDB, Open Weather, OpenTopoMap, OSM, Stamen, Strava, Wikimedia

.gitignore

@@ -18,7 +18,7 @@ examples/*.json
 examples/*.qml
 symbology-style.db
 # enmapbox/exampledata/*.gpkg
-
+splashscreen_tmp.*
 
 # we do not like to have compiled qt resource files in our repository!
 *_rc.py

.plugin.ini

@@ -1,6 +1,6 @@
 [metadata]
 name = EnMAP-Box 3
-version = 3.15-alpha.0
+version = 3.16-alpha.0
 qgisMinimumVersion = 3.34
 description = Imaging Spectroscopy and Remote Sensing for QGIS
 tags =
@@ -80,6 +80,7 @@ include =
     rx:enmapboxexternal/.*\.(py)
     enmapboxplugins/*
     enmapboxgeoalgorithms/*
+    enmapbox/gui/splashscreen/splashscreen.png
     __init__.py
     CHANGELOG.rst
     CHANGELOG.md

CHANGELOG.md

@@ -1,4 +1,42 @@
 # CHANGELOG
+## Version 3.15 (2024-10-01)
+_This release was tested under QGIS 3.34 (LTR) and 3.38 (latest release)._
+### New Features
+#### Applications
+* add algorithm and interactive tool for plotting trajectories of land cover change over time via Sankey plot [#924](https://github.com/EnMAP-Box/enmap-box/issues/924)
+#### Data / Metadata Model
+* support temporal metadata provided by 'time' dimension in NetCDF files [#906](https://github.com/EnMAP-Box/enmap-box/issues/906)
+* support temporal metadata provided by .aux.json files created with  R-cran terra package [#907](https://github.com/EnMAP-Box/enmap-box/issues/907)
+#### GUI
+* [Data Views] add "Apply mask" option to the raster layer context menu [#942](https://github.com/EnMAP-Box/enmap-box/issues/942)
+#### Processing Algorithms
+* Import USGS ASCII Speclib [#302](https://github.com/EnMAP-Box/enmap-box/issues/302)
+* add import algorithms for Planet Scope products [#492](https://github.com/EnMAP-Box/enmap-box/issues/492)
+* [Classification workflow] support OOB validation [#910](https://github.com/EnMAP-Box/enmap-box/issues/910)
+* [Create classification/regression/unsupervised dataset] store sample locations inside a dataset if available [#911](https://github.com/EnMAP-Box/enmap-box/issues/911)
+* [Classification workflow] add "classification layer accuracy and area report" output [#912](https://github.com/EnMAP-Box/enmap-box/issues/912)
+* implement "Create spectral library (from classification dataset)" [#917](https://github.com/EnMAP-Box/enmap-box/issues/917)
+* add algorithm and interactive tool for plotting trajectories of land cover change over time via Sankey plot [#924](https://github.com/EnMAP-Box/enmap-box/issues/924)
+* add algorithms for creating spectral library from classification/regression dataset [#931](https://github.com/EnMAP-Box/enmap-box/issues/931)
+* [Raster layer bounding polygon] add option for convex hull [#950](https://github.com/EnMAP-Box/enmap-box/issues/950)
+* [Analysis ready data] add algorithm for raster tiling [#953](https://github.com/EnMAP-Box/enmap-box/issues/953)
+* add "Aggregate raster layers" algorithm [#956](https://github.com/EnMAP-Box/enmap-box/issues/956)
+* add algorithm for creating a raster mask [#959](https://github.com/EnMAP-Box/enmap-box/issues/959)
+* [Import EnMAP L2A product] support L2A Analysis Ready Data from Geoservice / EOLAB [#973](https://github.com/EnMAP-Box/enmap-box/issues/973)
+* [Import EnMAP L2A product] derive bad band information from metadata file [#974](https://github.com/EnMAP-Box/enmap-box/issues/974)
+* in all algorithms with VRT raster output, also support GTiff and ENVI outputs [#977](https://github.com/EnMAP-Box/enmap-box/issues/977)
+#### Miscellaneous
+* implement auto-generated changelog [#938](https://github.com/EnMAP-Box/enmap-box/issues/938)
+### Fixed Bugs
+<details><summary>Show all (5)</summary>
+
+* Save current profiles on CTRL+S [#871](https://github.com/EnMAP-Box/enmap-box/issues/871)
+* [Spectral resampling] EMIT sensor is missing [#891](https://github.com/EnMAP-Box/enmap-box/issues/891)
+* [Classification layer accuracy and area report (for simple random sampling)] wrong confidence intervals for area estimates [#909](https://github.com/EnMAP-Box/enmap-box/issues/909)
+* Regression based unmixing | problem with implementation of LinearSVR [#967](https://github.com/EnMAP-Box/enmap-box/issues/967)
+* [Regression-based unmixing] _catboost.CatBoostError: Expected callable object or stream-like object [#980](https://github.com/EnMAP-Box/enmap-box/issues/980)
+</details>
+
 ## Version 3.14 (2024-04-11)
 _This release was tested under QGIS 3.34 (LTR) and 3.36 (latest release)._
 ### New Features
@@ -30,7 +68,7 @@ _This release was tested under QGIS 3.34 (LTR) and 3.36 (latest release)._
 * [Scripts/EnFireMAP] add script for sampling point data from data cube [#681](https://github.com/EnMAP-Box/enmap-box/issues/681)
 * split and restructure the requirement.txt file by operating system and Python environment [#701](https://github.com/EnMAP-Box/enmap-box/issues/701)
 ### Fixed Bugs
-<details><summary>Show all</summary>
+<details><summary>Show all (39)</summary>
 
 * [GEE Time Series Explorer] AttributeError: 'GeeTemporalProfileDockWidget' object has no attribute 'onDownloadLayerProfilesClicked' [#691](https://github.com/EnMAP-Box/enmap-box/issues/691)
 * splash screen not showing up on EnMAP-Box startup [#714](https://github.com/EnMAP-Box/enmap-box/issues/714)
@@ -64,10 +102,13 @@ _This release was tested under QGIS 3.34 (LTR) and 3.36 (latest release)._
 * AttributeError: 'NoneType' object has no attribute 'highlightedVariables' [#863](https://github.com/EnMAP-Box/enmap-box/issues/863)
 * [RasterReader] open a WMS layer with "openWithGdal=False" isn't working [#865](https://github.com/EnMAP-Box/enmap-box/issues/865)
 * EnMAP L2A data isn't scaled correctly between 0 and 1 [#879](https://github.com/EnMAP-Box/enmap-box/issues/879)
+* [Scale/truncate/convert raster layer] algo is placed in the wrong algo group [#885](https://github.com/EnMAP-Box/enmap-box/issues/885)
 * Couldn't load plugin 'enmapboxplugin' due to an error when calling its classFactory() method  [#886](https://github.com/EnMAP-Box/enmap-box/issues/886)
 * [SpectralView] GeoJSON library with NaN values not correctly plotted [#887](https://github.com/EnMAP-Box/enmap-box/issues/887)
 * [Classification layer accuracy and area report] issue with unclassified pixel inside map [#900](https://github.com/EnMAP-Box/enmap-box/issues/900)
+* [Data Sources] right-click on nodes inside a model file (*.pkl) gives error [#908](https://github.com/EnMAP-Box/enmap-box/issues/908)
 * Spectral library axis flipped [#916](https://github.com/EnMAP-Box/enmap-box/issues/916)
+* [SpectralLibraryUtils] SpectralLibraryUtils.writeToSource is creating wrong CRS [#936](https://github.com/EnMAP-Box/enmap-box/issues/936)
 </details>
 
 ## Version 3.13 (2023-10-06)
@@ -123,7 +164,7 @@ _This release was tested under QGIS 3.28 (LTR), 3.32 and 3.34 (latest release)._
 * [Example Dataset Potsdam] add library and continuous-vector-layer [#576](https://github.com/EnMAP-Box/enmap-box/issues/576)
 * [Scripts] implement script for cutting EnMAP L2A scenes according to a given tiling scheme [#583](https://github.com/EnMAP-Box/enmap-box/issues/583)
 ### Fixed Bugs
-<details><summary>Show all</summary>
+<details><summary>Show all (62)</summary>
 
 * [Profile Analytics] ignore or handle WMS layers properly [#443](https://github.com/EnMAP-Box/enmap-box/issues/443)
 * [Scripts/create_plugin.py] can't build plugin (somehow related to Markdown) [#452](https://github.com/EnMAP-Box/enmap-box/issues/452)
@@ -227,7 +268,7 @@ _This release was tested under QGIS 3.28 (LTR)._
 * Reporting [#258](https://github.com/EnMAP-Box/enmap-box/issues/258)
 * make typeguard optional [#345](https://github.com/EnMAP-Box/enmap-box/issues/345)
 ### Fixed Bugs
-<details><summary>Show all</summary>
+<details><summary>Show all (69)</summary>
 
 * The setup for testing non-blocking-dependencies is gone. [#176](https://github.com/EnMAP-Box/enmap-box/issues/176)
 * CatBootRegressor issue [#189](https://github.com/EnMAP-Box/enmap-box/issues/189)
@@ -326,7 +367,7 @@ _This release was tested under QGIS 3.26._
 * Application path not initialized [#4](https://github.com/EnMAP-Box/enmap-box/issues/4)
 * RasterReader wavelength fails with FORCE TSI images [#9](https://github.com/EnMAP-Box/enmap-box/issues/9)
 ### Fixed Bugs
-<details><summary>Show all</summary>
+<details><summary>Show all (49)</summary>
 
 * link extraction from glossary.rst is broken [#1](https://github.com/EnMAP-Box/enmap-box/issues/1)
 * temporal pixel profile from FORCE TSI raster not correctly displayed in SpectralView [#5](https://github.com/EnMAP-Box/enmap-box/issues/5)

CONTRIBUTORS.md

@@ -3,25 +3,28 @@ People who made large contributions to the EnMAP-Box (in alphabetical order).
 ### Earth Observation Lab, Humboldt-Universität zu Berlin, Germany
 
 * Andreas Janz <[email protected]>
-* Akpona Okujeni <[email protected]>
+* Akpona Okujeni
 * Benjamin Jakimow <[email protected]>
-* Franz Schug <[email protected]>
-* Katja Kowalski <[email protected]>
-* Philippe Rufin <[email protected]>
-* Marcel Schwieder <[email protected]>
-* Matthias Held <[email protected]>
-* Sam Cooper <[email protected]>
-* Stefan Ernst <[email protected]>
+* Franz Schug
+* Katja Kowalski
+* Philippe Rufin
+* Marcel Schwieder
+* Matthias Held
+* Sam Cooper
+* Stefan Ernst
 
 ### Earth Observation and Geoinformation Science Lab, University of Greifswald, Germany
 
-* Fabian Thiel <[email protected]>
+* Fabian Thiel
 * Sebastian van der Linden <[email protected]>
 
 ### Ludwig-Maximilians-Universität München, Germany
 
-* Matthias Wocher <[email protected]>
-* Martin Danner
+* Katja Berger <[email protected]>
+* Matthias Wocher <[email protected]>
+* Martin Danner <[email protected]>
+* Stefanie Steinhauser <[email protected]>
+* Tobias Hank <[email protected]>
 
 ### GFZ German Research Centre For Geosciences, Potsdam, Germany
 
@@ -43,6 +46,6 @@ People who made large contributions to the EnMAP-Box (in alphabetical order).
 ### AWI Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
 
 * Astrid Bracher <[email protected]>
-* Brenner Silva <[email protected]>
-* Leonardo Alvarado <leonardo.alvarado@awi.de>
+* Brenner Silva
+* Leonardo Alvarado  <leonardo.alvarado@dlr.de>
 * Mariana Altenburg Soppa <[email protected]>

enmapbox/__init__.py

@@ -34,10 +34,9 @@
 import warnings
 
 from osgeo import gdal
-
 from qgis.PyQt.QtCore import QSettings
 from qgis.PyQt.QtGui import QIcon
-from qgis.core import Qgis, QgsApplication, QgsProcessingRegistry, QgsProcessingProvider, QgsProcessingAlgorithm
+from qgis.core import Qgis, QgsApplication, QgsProcessingAlgorithm, QgsProcessingProvider, QgsProcessingRegistry
 from qgis.gui import QgisInterface, QgsMapLayerConfigWidgetFactory
 
 # provide shortcuts
@@ -96,7 +95,6 @@
 
 ENMAP_BOX_KEY = 'EnMAP-Box'
 
-_ENMAPBOX_PROCESSING_PROVIDER: QgsProcessingProvider = None
 _ENMAPBOX_MAPLAYER_CONFIG_WIDGET_FACTORIES: typing.List[QgsMapLayerConfigWidgetFactory] = []
 
 gdal.SetConfigOption('GDAL_VRT_ENABLE_PYTHON', 'YES')
@@ -262,13 +260,11 @@ def registerEnMAPBoxProcessingProvider():
     assert isinstance(registry, QgsProcessingRegistry)
     provider = registry.providerById(ID)
     if not isinstance(provider, QgsProcessingProvider):
-        provider = EnMAPBoxProcessingProvider()
+        provider = EnMAPBoxProcessingProvider.instance()
         registry.addProvider(provider)
 
     assert isinstance(provider, EnMAPBoxProcessingProvider)
     assert id(registry.providerById(ID)) == id(provider)
-    global _ENMAPBOX_PROCESSING_PROVIDER
-    _ENMAPBOX_PROCESSING_PROVIDER = provider
 
     try:
         existingAlgNames = [a.name() for a in registry.algorithms() if a.groupId() == provider.id()]
@@ -293,8 +289,7 @@ def unregisterEnMAPBoxProcessingProvider():
     provider = registry.providerById(ID)
 
     if isinstance(provider, EnMAPBoxProcessingProvider):
-        global _ENMAPBOX_PROCESSING_PROVIDER
-        _ENMAPBOX_PROCESSING_PROVIDER = None
+        EnMAPBoxProcessingProvider._ENMAPBOX_PROCESSING_PROVIDER = None
         # this deletes the C++ object
         registry.removeProvider(ID)
 

enmapbox/algorithmprovider.py

@@ -50,6 +50,15 @@ class EnMAPBoxProcessingProvider(QgsProcessingProvider):
     It enhances the "standard" processing.core.AlgorithmProvider by functionality to add and remove GeoAlgorithms during runtime.
     """
 
+    _ENMAPBOX_PROCESSING_PROVIDER = None
+
+    @staticmethod
+    def instance() -> 'EnMAPBoxProcessingProvider':
+
+        if EnMAPBoxProcessingProvider._ENMAPBOX_PROCESSING_PROVIDER is None:
+            EnMAPBoxProcessingProvider._ENMAPBOX_PROCESSING_PROVIDER = EnMAPBoxProcessingProvider()
+        return EnMAPBoxProcessingProvider._ENMAPBOX_PROCESSING_PROVIDER
+
     def __init__(self):
         super(EnMAPBoxProcessingProvider, self).__init__()
         # internal list of GeoAlgorithms. Is used on re-loads and can be manipulated

enmapbox/apps/lmuvegetationapps/IVVRM/IVVRM_GUI.py

@@ -975,7 +975,7 @@ def read_file(self):
                 self.gui.tablePreview.setItem(row, col, item_wl)          # place wavelength item
                 self.gui.tablePreview.setItem(row, col + 1, item_weigh)   # place weight item
 
-        self.gui.tablePreview.horizontalHeader().setResizeMode(QHeaderView.ResizeToContents)
+        self.gui.tablePreview.horizontalHeader().setSectionResizeMode(QHeaderView.ResizeToContents)
         self.flag_srf = True
         self.flag_image = False
         self.check_flags()  # check if the app is ready to be run

enmapbox/apps/lmuvegetationapps/LUT/CreateLUT_GUI.py

@@ -1220,7 +1220,7 @@ def read_file(self):
                 self.gui.tablePreview.setItem(row, col, item_wl)          # place wavelength item
                 self.gui.tablePreview.setItem(row, col + 1, item_weigh)   # place weight item
 
-        self.gui.tablePreview.horizontalHeader().setResizeMode(QHeaderView.ResizeToContents)
+        self.gui.tablePreview.horizontalHeader().setSectionResizeMode(QHeaderView.ResizeToContents)
         self.flag_srf = True
         self.flag_image = False
         self.check_flags()  # check if the app is ready to be run
@@ -1297,7 +1297,7 @@ def image_read(self): # read only necessary info: fwhm and center wavelengths
         for i in self.outreach:
             self.gui.tablePreview.item(i, 0).setBackground(QColor(200, 0, 0))
         self.gui.tablePreview.setHorizontalHeaderLabels(header_items)
-        self.gui.tablePreview.horizontalHeader().setResizeMode(QHeaderView.ResizeToContents)
+        self.gui.tablePreview.horizontalHeader().setSectionResizeMode(QHeaderView.ResizeToContents)
         wavelength_srf = np.delete(wavelength, self.outreach)
         fwhm_srf = np.delete(fwhm, self.outreach)
         self.x = np.array(list(zip(wavelength_srf, fwhm_srf)))

enmapbox/apps/lmuvegetationapps/Processor/Processor_Inversion_GUI.py

@@ -100,7 +100,7 @@ def initial_values(self):
         self.out_image = None  # File for output results
         self.out_mode = 'single'  # 'single' all PROSAIL parameters in one file as bands, 'individual' one file per para
 
-        self.geo_mode = "file"  # Is the geometry (SZA, OZA, rAA) suplied through 'file' or are they 'fix'
+        self.geo_mode = "fix"  # Is the geometry (SZA, OZA, rAA) suplied through 'file' or are they 'fix'
         self.geo_file = None  # if geo_mode == 'file', which is the path?
         self.geo_fixed = [None]*3  # if geo_mode == 'fix', which are the three geometry angles?
 
@@ -112,6 +112,7 @@ def initial_values(self):
         self.gui.mLayerMask.setLayer(None)
 
         self.algorithm = None
+        self.gpr_flag = False
 
         # Initial Model is set to EnMAP as default
         self.model_meta_file = os.path.join(APP_DIR, 'Resources/Processor/EnMAP.meta')
@@ -306,13 +307,15 @@ def open_file(self, mode):
                 self.mask_image = None
                 return
 
-        elif mode == "model":  # Select algorithm for inversion my picking its Meta-file (*.meta)
+        elif mode == "model":  # Select algorithm for inversion by picking its Meta-file (*.meta)
             result = str(QFileDialog.getOpenFileName(caption='Select Machine Learning Model',
                                                      filter="Processor META File (*.meta)")[0])
             if not result:
                 return
             self.meta_dict = self._get_processor_meta(file=result)
             self.algorithm = self.meta_dict['alg']
+            if self.algorithm == 'GPR':
+                self.gpr_flag = True
 
             targets = self.meta_dict.get('target_parameters')
             if isinstance(targets, str):
@@ -628,7 +631,7 @@ def run_inversion(self):
                                                mask_ndvi=self.mask_ndvi, ndvi_thr=self.ndvi_thr,
                                                ndvi_bands=self.ndvi_bands, mask_image=self.mask_image,
                                                geo_in=self.geo_file, fixed_geos=self.geo_fixed,
-                                               spatial_geo=self.spatial_geo, paras=self.paras)
+                                               spatial_geo=self.spatial_geo, paras=self.paras, gpr_flag=self.gpr_flag)
         except ValueError as e:
             self.abort(message="Failed to setup inversion: {}".format(str(e)))
             return
@@ -656,11 +659,13 @@ def run_inversion(self):
             self.abort(message="An error occurred while trying to write output-image: {}".format(str(e)))
             return
 
+        if self.gpr_flag is True:
+            proc.predict_main.write_prediction_std()
+
         self.prg_widget.gui.lblCancel.setText("")
         self.prg_widget.gui.allow_cancel = True
         self.prg_widget.gui.close()
         QMessageBox.information(self.gui, "Finish", "ML mapping finished")
-        self.gui.close()
 
     def open_train_gui(self):
         # Open the GUI for training new models