Merge pull request #127 from GispoCoding/126-add-documentation-to-tra…

…nsformation-processing-algorithms

Added documentation to transformation processing algorithms

eis_qgis_plugin/processing/algorithms/transformations/alr_transform.py

@@ -21,32 +21,34 @@ def __init__(self) -> None:
     def initAlgorithm(self, config=None):
         self.alg_parameters = ["input_vector", "column", "keep_denominator_column", "output_vector"]
 
-        self.addParameter(
-            QgsProcessingParameterFeatureSource(
-                name=self.alg_parameters[0], description="Input vector"
-            )
+        input_vector_param = QgsProcessingParameterFeatureSource(
+            name=self.alg_parameters[0], description="Input vector"
         )
-
-        self.addParameter(
-            QgsProcessingParameterField(
-                name=self.alg_parameters[1],
-                description="Denominator column",
-                parentLayerParameterName=self.alg_parameters[0],
-                optional=True,
-            )
+        input_vector_param.setHelp("Input vector with compositional data.")
+        self.addParameter(input_vector_param)
+
+        denominator_column_param = QgsProcessingParameterField(
+            name=self.alg_parameters[1],
+            description="Denominator column",
+            parentLayerParameterName=self.alg_parameters[0],
+            optional=True,
         )
+        denominator_column_param.setHelp("The column to be used as the denominator column.")
+        self.addParameter(denominator_column_param)
 
-        self.addParameter(
-            QgsProcessingParameterBoolean(
-                name=self.alg_parameters[2],
-                description="Keep denominator column",
-                defaultValue=False
-            )
+        keep_denominator_column_param = QgsProcessingParameterBoolean(
+            name=self.alg_parameters[2],
+            description="Keep denominator column",
+            defaultValue=False
+        )
+        keep_denominator_column_param.setHelp(
+            "Whether to include the used denominator column in the result."
         )
+        self.addParameter(keep_denominator_column_param)
 
-        self.addParameter(
-            QgsProcessingParameterVectorDestination(
-                name=self.alg_parameters[3],
-                description="Output vector",
-            )
+        output_vector_param = QgsProcessingParameterVectorDestination(
+            name=self.alg_parameters[3],
+            description="Output vector",
         )
+        output_vector_param.setHelp("Output vector with the ALR transformed data.")
+        self.addParameter(output_vector_param)

eis_qgis_plugin/processing/algorithms/transformations/binarize.py

@@ -15,28 +15,33 @@ def __init__(self) -> None:
         self._display_name = "Binarize"
         self._group = "Transformations"
         self._group_id = "transformations"
-        self._short_help_string = "Calculate binarize transformation for data"
+        self._short_help_string = """
+            Binarize data based on a given threshold.
+
+            Replaces values less or equal threshold with 0. \
+            Replaces values greater than the threshold with 1.
+        """
 
     def initAlgorithm(self, config=None):
         self.alg_parameters = ["input_raster", "threshold", "output_raster"]
-
-        self.addParameter(
-            QgsProcessingParameterRasterLayer(
-                name=self.alg_parameters[0], description="Input raster"
-            )
+
+        input_vector_param = QgsProcessingParameterRasterLayer(
+            name=self.alg_parameters[0], description="Input raster"
         )
+        input_vector_param.setHelp("Input raster to be binarized.")
+        self.addParameter(input_vector_param)
 
-        self.addParameter(
-            QgsProcessingParameterNumber(
-                name=self.alg_parameters[1],
-                description="Binarizing threshold",
-                type=QgsProcessingParameterNumber.Double,
-            )
+        binarizing_threshold_param = QgsProcessingParameterNumber(
+            name=self.alg_parameters[1],
+            description="Binarizing threshold",
+            type=QgsProcessingParameterNumber.Double,
         )
+        binarizing_threshold_param.setHelp("Threshold value for binarization.")
+        self.addParameter(binarizing_threshold_param)
 
-        self.addParameter(
-            QgsProcessingParameterRasterDestination(
-                name=self.alg_parameters[2],
-                description="Output raster",
-            )
+        output_raster_param = QgsProcessingParameterRasterDestination(
+            name=self.alg_parameters[2],
+            description="Output raster",
         )
+        output_raster_param.setHelp("Output raster with transformed data.")
+        self.addParameter(output_raster_param)

eis_qgis_plugin/processing/algorithms/transformations/clip_transform.py

@@ -15,9 +15,12 @@ def __init__(self) -> None:
         self._display_name = "Clip transform"
         self._group = "Transformations"
         self._group_id = "transformations"
-        self._short_help_string = (
-            "Clips data based on specified upper and lower limits."
-        )
+        self._short_help_string = """
+            Clips data based on specified upper and lower limits.
+
+            Replaces values below the lower limit and above the upper limit with provided values, respecively.
+            Works both one-sided and two-sided but raises error if no limits provided.
+        """
 
     def initAlgorithm(self, config=None):
         self.alg_parameters = [
@@ -27,32 +30,32 @@ def initAlgorithm(self, config=None):
             "output_raster",
         ]
 
-        self.addParameter(
-            QgsProcessingParameterRasterLayer(
-                name=self.alg_parameters[0], description="Input raster"
-            )
+        input_raster_param = QgsProcessingParameterRasterLayer(
+            name=self.alg_parameters[0], description="Input raster"
         )
-
-        self.addParameter(
-            QgsProcessingParameterNumber(
-                name=self.alg_parameters[1],
-                description="Lower",
-                type=QgsProcessingParameterNumber.Double,
-                optional=True,
-            )
+        input_raster_param.setHelp("Input raster to be clipped.")
+        self.addParameter(input_raster_param)
+
+        lower_limit_param = QgsProcessingParameterNumber(
+            name=self.alg_parameters[1],
+            description="Lower",
+            type=QgsProcessingParameterNumber.Double,
+            optional=True,
         )
-
-        self.addParameter(
-            QgsProcessingParameterNumber(
-                name=self.alg_parameters[2],
-                description="Higher",
-                type=QgsProcessingParameterNumber.Double,
-                optional=True,
-            )
+        lower_limit_param.setHelp("Lower transformation limit.")
+        self.addParameter(lower_limit_param)
+
+        higher_limit_param = QgsProcessingParameterNumber(
+            name=self.alg_parameters[2],
+            description="Higher",
+            type=QgsProcessingParameterNumber.Double,
+            optional=True,
         )
+        higher_limit_param.setHelp("Higher transformation limit.")
+        self.addParameter(higher_limit_param)
 
-        self.addParameter(
-            QgsProcessingParameterRasterDestination(
-                name=self.alg_parameters[3], description="Output raster"
-            )
+        output_raster_param = QgsProcessingParameterRasterDestination(
+            name=self.alg_parameters[3], description="Output raster"
         )
+        output_raster_param.setHelp("Output raster with transformed data.")
+        self.addParameter(output_raster_param)

eis_qgis_plugin/processing/algorithms/transformations/clr_transform.py

@@ -19,15 +19,15 @@ def __init__(self) -> None:
     def initAlgorithm(self, config=None):
         self.alg_parameters = ["input_vector", "output_vector"]
 
-        self.addParameter(
-            QgsProcessingParameterFeatureSource(
-                name=self.alg_parameters[0], description="Input vector"
-            )
+        input_vector_param = QgsProcessingParameterFeatureSource(
+            name=self.alg_parameters[0], description="Input vector"
         )
+        input_vector_param.setHelp("Input vector with compositional data.")
+        self.addParameter(input_vector_param)
 
-        self.addParameter(
-            QgsProcessingParameterVectorDestination(
-                name=self.alg_parameters[1],
-                description="Output vector",
-            )
+        output_vector_param = QgsProcessingParameterVectorDestination(
+            name=self.alg_parameters[1],
+            description="Output vector",
         )
+        output_vector_param.setHelp("Output vector with the CLR transformed data.")
+        self.addParameter(output_vector_param)

eis_qgis_plugin/processing/algorithms/transformations/inverse_alr_transform.py

@@ -18,35 +18,37 @@ def __init__(self) -> None:
         self._group_id = "transformations"
         self._short_help_string = "Perform the inverse transformation for a set of ALR transformed data."
 
-
     def initAlgorithm(self, config=None):
         self.alg_parameters = ["input_vector", "denominator_column", "scale", "output_vector"]
 
-        self.addParameter(
-            QgsProcessingParameterFeatureSource(
-                name=self.alg_parameters[0], description="Input vector"
-            )
+        input_vector_param = QgsProcessingParameterFeatureSource(
+            name=self.alg_parameters[0], description="Input vector"
         )
+        input_vector_param.setHelp("Input vector with ALR transformed compositional data.")
+        self.addParameter(input_vector_param)
 
-        self.addParameter(
-            QgsProcessingParameterString(
-                name=self.alg_parameters[1],
-                description="Denominator column name",
-            )
+        denominator_column_name_param = QgsProcessingParameterString(
+            name=self.alg_parameters[1],
+            description="Denominator column name",
         )
-
-        self.addParameter(
-            QgsProcessingParameterNumber(
-                name=self.alg_parameters[2],
-                description="Scale",
-                defaultValue=1.0,
-                type=QgsProcessingParameterNumber.Double
-            )
+        denominator_column_name_param.setHelp("The name of the denominator column.")
+        self.addParameter(denominator_column_name_param)
+
+        scale_param = QgsProcessingParameterNumber(
+            name=self.alg_parameters[2],
+            description="Scale",
+            defaultValue=1.0,
+            type=QgsProcessingParameterNumber.Double
+        )
+        scale_param.setHelp(
+            "The value to which each composition should be normalized. \
+            Eg., if the composition is expressed as percentages, scale=100."
         )
+        self.addParameter(scale_param)
 
-        self.addParameter(
-            QgsProcessingParameterVectorDestination(
-                name=self.alg_parameters[3],
-                description="Output vector",
-            )
+        output_vector_param = QgsProcessingParameterVectorDestination(
+            name=self.alg_parameters[3],
+            description="Output vector",
         )
+        output_vector_param.setHelp("Output vector with inverse transformed data.")
+        self.addParameter(output_vector_param)

eis_qgis_plugin/processing/algorithms/transformations/inverse_clr_transform.py

@@ -17,28 +17,31 @@ def __init__(self) -> None:
         self._group_id = "transformations"
         self._short_help_string = "Perform the inverse transformation for a set of CLR transformed data."
 
-
     def initAlgorithm(self, config=None):
         self.alg_parameters = ["input_vector", "scale", "output_vector"]  # NOTE: Colnames param omitted
 
-        self.addParameter(
-            QgsProcessingParameterFeatureSource(
-                name=self.alg_parameters[0], description="Input vector"
-            )
+        input_vector_param = QgsProcessingParameterFeatureSource(
+            name=self.alg_parameters[0], description="Input vector"
         )
-
-        self.addParameter(
-            QgsProcessingParameterNumber(
-                name=self.alg_parameters[1],
-                description="Scale",
-                defaultValue=1.0,
-                type=QgsProcessingParameterNumber.Double
-            )
+        input_vector_param.setHelp("Input vector with CLR transformed compositional data.")
+        self.addParameter(input_vector_param)
+
+        scale_param = QgsProcessingParameterNumber(
+            name=self.alg_parameters[1],
+            description="Scale",
+            defaultValue=1.0,
+            type=QgsProcessingParameterNumber.Double
         )
+        scale_param.setHelp(
+            "The value to which each composition should be normalized. \
+            Eg., if the composition is expressed as percentages, scale=100."
+        )
+        self.addParameter(scale_param)
 
-        self.addParameter(
-            QgsProcessingParameterVectorDestination(
-                name=self.alg_parameters[2],
-                description="Output vector",
-            )
+        output_vector_param = QgsProcessingParameterVectorDestination(
+            name=self.alg_parameters[2],
+            description="Output vector",
         )
+        output_vector_param.setHelp("Output vector with inverse transformed data.")
+        self.addParameter(output_vector_param)
+

eis_qgis_plugin/processing/algorithms/transformations/log_transform.py

@@ -15,29 +15,27 @@ def __init__(self) -> None:
         self._display_name = "Logarithmic transform"
         self._group = "Transformations"
         self._group_id = "transformations"
-        self._short_help_string = (
-            "Perform a logarithmic transformation on the provided data."
-        )
+        self._short_help_string = "Perform a logarithmic transformation on the provided data."
 
     def initAlgorithm(self, config=None):
         self.alg_parameters = ["input_raster", "log_type", "output_raster"]
 
-        self.addParameter(
-            QgsProcessingParameterRasterLayer(
-                name=self.alg_parameters[0], description="Input raster"
-            )
+        input_raster_param =  QgsProcessingParameterRasterLayer(
+            name=self.alg_parameters[0], description="Input raster"
         )
+        input_raster_param.setHelp("Input raster to be transformed.")
+        self.addParameter(input_raster_param)
 
-        self.addParameter(
-            QgsProcessingParameterEnum(
-                name=self.alg_parameters[1],
-                description="Lower",
-                options=["log2", "log10", "ln"],
-            )
+        log_type_param =  QgsProcessingParameterEnum(
+            name=self.alg_parameters[1],
+            description="Log type",
+            options=["log2", "log10", "ln"],
         )
+        log_type_param.setHelp("The base for logarithmic transformation.")
+        self.addParameter(log_type_param)
 
-        self.addParameter(
-            QgsProcessingParameterRasterDestination(
-                name=self.alg_parameters[2], description="Output raster"
-            )
+        output_raster_param = QgsProcessingParameterRasterDestination(
+            name=self.alg_parameters[2], description="Output raster"
         )
+        output_raster_param.setHelp("Output raster with transformed data.")
+        self.addParameter(output_raster_param)