update documentation

mfroeling · Dec 22, 2023 · 54b76c9 · 54b76c9
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diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/$LoadedColor.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/$LoadedColor.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/ActivationType.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/ActivationType.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/AddScientificColours.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/AddScientificColours.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/AllowSelfDependencies.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/AllowSelfDependencies.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/DixonConstrainPhase.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/DixonConstrainPhase.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/DixonFixT2.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/DixonFixT2.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/DixonPhases.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/DixonPhases.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/ExtractColorData.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/ExtractColorData.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/GenerateAmps.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/GenerateAmps.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/GetTractMeans.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/GetTractMeans.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/LabelPlacement.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/LabelPlacement.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/PCAComplex.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/PCAComplex.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/PhaseEchos.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/PhaseEchos.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/ScientificColorData.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/ScientificColorData.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/SelectSegmentations.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/SelectSegmentations.nb
diff --git a/QMRITools/Documentation/English/ReferencePages/Symbols/tempDir.nb b/QMRITools/Documentation/English/ReferencePages/Symbols/tempDir.nb
diff --git a/QMRITools/Kernel/DenoiseTools.wl b/QMRITools/Kernel/DenoiseTools.wl
@@ -114,7 +114,7 @@ PCAClipping::usage =
 PCANoiseSigma::usage = 
 "PCANoiseSigma is an option of DenoiseCSIdata and can be \"Corners\" or \"Automatic\"."
 
-PCAComplex::uasge = 
+PCAComplex::usage = 
 "PCAComplex is an option of PCADeNoise and can be True of False. If set true the input data is expexted to be {real, imag}."
 
 

diff --git a/QMRITools/Kernel/DixonTools.wl b/QMRITools/Kernel/DixonTools.wl
@@ -124,7 +124,7 @@ DixonIterations::usage =
 "DixonIterations is an options for DixonReconstruct. Defines the maximum itterations the fit can use."
 
 DixonPhases::usage = 
-"DixonBipolar is an option for DixonReconstruct. It defines which phases to fit within the model.
+"DixonPhases is an option for DixonReconstruct. It defines which phases to fit within the model.
 The order is {T2*, B0, bipolar, initial, bipolar}."
 
 PhaseEchos::usage = 

diff --git a/QMRITools/Kernel/GeneralTools.wl b/QMRITools/Kernel/GeneralTools.wl
@@ -310,10 +310,10 @@ MonitorCalc::usage =
 
 
 LabelPlacement::usage =
-"LabelPlacement ..."
+"LabelPlacement is an option for MakeFunctionGraph. Defines where to place the label of the functiongraph. Accepts values that can be used in Placed."
 
 AllowSelfDependencies::usage = 
-"AllowSelfDependencies ..."
+"AllowSelfDependencies is and option for MakeFunctionGraph. Can be True or False. If True a function that calls itself is also shown."
 
 
 (* ::Subsection::Closed:: *)

diff --git a/QMRITools/Kernel/MaskingTools.wl b/QMRITools/Kernel/MaskingTools.wl
@@ -70,7 +70,7 @@ MergeSegmentations::usage =
 Output is a labled segmentation."
 
 SelectSegmentations::usage=
-"SelectSegmentations[seg, lab]..."
+"SelectSegmentations[seg, labs] selects only the segmentaions with label number labs."
 
 SmoothSegmentation::usage =
 "SmoothSegmentation[masks] smooths segmentations and removes the overlaps between multiple segmentations." 

diff --git a/QMRITools/Kernel/ProcessingTools.wl b/QMRITools/Kernel/ProcessingTools.wl
@@ -64,7 +64,7 @@ Mask can be genereated by SegmentTracts.
 GetMaskMeans[dat, mask, name] where name is a string that is added to the header."
 
 
-GetTractMeans::usge = 
+GetTractMeans::usage = 
 "GetTractMeans[dat, tracts, vox] calculates the mean, std, 5,50 and 95% CI form the given data for each of the given tracts. 
 Tracts can be by SplitSegmentations. name is a string that is added to the header.
 

diff --git a/QMRITools/Kernel/ScientificColorData.wl b/QMRITools/Kernel/ScientificColorData.wl
@@ -25,10 +25,10 @@ BeginPackage["QMRITools`ScientificColorData`"];
 
 
 AddScientificColours::usage = 
-"AddScientificColours[dir]..."
+"AddScientificColours[dir] adds the scientific colour data (https://zenodo.org/records/8409685) from the specified folder."
 
 ExtractColorData::usage = 
-"ExtractColorData[] Extracts the scientific colordata archive."
+"ExtractColorData[] Extracts the scientific colordata archive (https://zenodo.org/records/8409685)."
 
 
 (* ::Subsection:: *)

diff --git a/QMRITools/Kernel/SegmentationTools.wl b/QMRITools/Kernel/SegmentationTools.wl
@@ -177,7 +177,7 @@ InputFilters::usage =
 "InputFilters is an option for MakeUnet. It defines the amount of convolutional filters of the the first UNET block."
 
 ActivationType::usage = 
-"InputFilters is an option for MakeUnet. It sepecifies which activation layer is used in the network. It can be \"LeakyRELU\" or any type allowed 
+"ActivationType is an option for MakeUnet. It sepecifies which activation layer is used in the network. It can be \"LeakyRELU\" or any type allowed 
 by a \"name\" definition in ElementwiseLayer."