Merge pull request #196 from DimitriPapadopoulos/codespell

Fix typos found by codespell

specification/samples/2013-06/transformations-downgrade.ome.xml

@@ -26,7 +26,7 @@
 
   <OME:ExperimenterGroup Name="MyGroup" ID="ExperimenterGroup:1">
     <OME:Description>A description for my group.
-      Complete with basic formating, like new lines.</OME:Description>
+      Complete with basic formatting, like new lines.</OME:Description>
     <OME:ExperimenterRef ID="Experimenter:3"/>
     <OME:Leader ID="Experimenter:1"/>
     <OME:Leader ID="Experimenter:2"/>

specification/samples/2015-01/transformations-downgrade.ome.xml

@@ -26,7 +26,7 @@
   <OME:Experimenter ID="Experimenter:17"/>
 
   <OME:ExperimenterGroup Name="MyGroup" ID="ExperimenterGroup:1">
-    <OME:Description>A description for my group. Complete with basic formating, like new
+    <OME:Description>A description for my group. Complete with basic formatting, like new
       lines.</OME:Description>
     <OME:ExperimenterRef ID="Experimenter:3"/>
     <OME:Leader ID="Experimenter:1"/>

specification/samples/2016-06/transformations-downgrade.ome.xml

@@ -21,7 +21,7 @@
   <Experimenter ID="Experimenter:17"/>
 
   <ExperimenterGroup Name="MyGroup" ID="ExperimenterGroup:1">
-    <Description>A description for my group. Complete with basic formating, like new
+    <Description>A description for my group. Complete with basic formatting, like new
       lines.</Description>
     <ExperimenterRef ID="Experimenter:3"/>
     <Leader ID="Experimenter:1"/>

specification/src/main/java/ome/specification/SchemaResolver.java

@@ -96,7 +96,7 @@ public SchemaResolver() throws InstantiationException
           }
         }
 
-        // if verson 4 & 5 ?
+        // if version 4 & 5 ?
         if (theDOMImplementationLS == null) {
           try {
             System.setProperty(

specification/src/main/resources/released-schema/2003-FC/AnalysisModule.xsd

@@ -85,7 +85,7 @@
 	</element>
 	<element name = "FormalInput">
 		<annotation>
-			<documentation>Specifies an input requirement for a module. Image dimensions and image file locations (repository or other format) should not be specified with this. Image dimensions are intrisic to an image. They do not represent a special requirement. Image file locations and contents are specified by other elements. Specifically, RawImageFile, RawImageFilePath, XYPlaneFile, and XYPlaneFilePath.
+			<documentation>Specifies an input requirement for a module. Image dimensions and image file locations (repository or other format) should not be specified with this. Image dimensions are intrinsic to an image. They do not represent a special requirement. Image file locations and contents are specified by other elements. Specifically, RawImageFile, RawImageFilePath, XYPlaneFile, and XYPlaneFilePath.
 			</documentation>
 		</annotation>
 		<complexType>
@@ -303,7 +303,7 @@ Tied to DB. PROGRAMS.NEW_FEATURE_TAG
 	</element>
 	<element name = "InstallationScript">
 		<annotation>
-			<documentation>The script should interface with the OME API to find all information it needs. (i.e. installation path) It also needs to set the location of the program after the program is installed. The location should be set through the API, but it will propogate to the LOCATION column of the PROGRAMS table.</documentation>
+			<documentation>The script should interface with the OME API to find all information it needs. (i.e. installation path) It also needs to set the location of the program after the program is installed. The location should be set through the API, but it will propagate to the LOCATION column of the PROGRAMS table.</documentation>
 		</annotation>
 		<complexType>
 			<sequence>
@@ -376,7 +376,7 @@ A single program may have multiple interfaces. Why do you need multiple interfac
 Pretend you have a program that calculates simple statistics on the pixels of an image. You can specify which statistics you want via parameters.
 Typing
 ./stats -mean -sigma image1
-will ouput
+will output
 Image | mean | sigma
 image1 12.4 1
 Typing
@@ -385,7 +385,7 @@ will output
 Image | geomean | mean
 image1 12.2 12.4
 The outputs are completely different. You need to specify an interface for each of these behaviors.
-Or pretend you have a powerful program that can do 10 unrelated tasks, each of which outputs an image. While the outputs are the same type and format, they represent 10 completely different things. In this case, it might make sense to define 10 corrosponding AnalysisModule to represent the 10 logical functions.
+Or pretend you have a powerful program that can do 10 unrelated tasks, each of which outputs an image. While the outputs are the same type and format, they represent 10 completely different things. In this case, it might make sense to define 10 corresponding AnalysisModule to represent the 10 logical functions.
 In any case, use AnalysisModule to define an interface and Program to store installation software for a program.
 			</documentation>
 		</annotation>
@@ -445,7 +445,7 @@ A temporary hack to be sure, but that's the way it works for now.
 			</sequence>
 			<attribute name = "Path" use = "required">
 				<annotation>
-					<documentation>Categories are organized into heirarchical structures. This specifies the full path of this category in the following format.
+					<documentation>Categories are organized into hierarchical structures. This specifies the full path of this category in the following format.
 Path = "GrandParent name.Parent name.Category name"
 If you defined a sub category, we Strongly encourage you to also define all ancestor categories that are not part of the core OME specification.
 					</documentation>

specification/src/main/resources/released-schema/2003-FC/BinaryFile.xsd

@@ -34,7 +34,7 @@
 	<element name = "External">
 		<annotation>
 			<documentation>Describes a file location.  Can optionally specify a portion of a file using Offset and a ReadLength.
-If Offset and ReadLength are specified in conjuction with Compression, then they point into the uncompressed file.
+If Offset and ReadLength are specified in conjunction with Compression, then they point into the uncompressed file.
 			</documentation>
 		</annotation>
 		<complexType>

specification/src/main/resources/released-schema/2003-FC/CLI.xsd

@@ -229,8 +229,8 @@ Currently, only native image pixels are supported.
 			<attribute name = "Format">
 				<annotation>
 					<documentation>Specifies the expected format of the plane.
-RAW corrosponds to OME repository format of pixel dump.
-TIFF corrosponds to TIFF files.
+RAW corresponds to OME repository format of pixel dump.
+TIFF corresponds to TIFF files.
 Currently only TIFF is supported.
 					</documentation>
 				</annotation>
@@ -308,14 +308,14 @@ e.g. /OME/repository/1-tinyTest.ori
 			<attribute name = "RepeatCount" type = "positiveInteger">
 				<annotation>
 					<documentation>RepeatCount specifies how many times to read a record. If it is not specified, reading will continue until it reaches the end of the output stream.
-If used in conjuction with TerminateAt, reading will stop after RepeatCount or TerminateAt, whichever comes first.
+If used in conjunction with TerminateAt, reading will stop after RepeatCount or TerminateAt, whichever comes first.
 					</documentation>
 				</annotation>
 			</attribute>
 			<attribute name = "TerminateAt" type = "string">
 				<annotation>
 					<documentation>TerminateAt specifies a regular expression. When a match to this is found, reading will stop.
-If used in conjuction with RepeatCount, reading will stop after RepeatCount or TerminateAt, whichever comes first.
+If used in conjunction with RepeatCount, reading will stop after RepeatCount or TerminateAt, whichever comes first.
 					</documentation>
 				</annotation>
 			</attribute>
@@ -422,7 +422,7 @@ This means a stack statistics record that specifies theC as an index before theT
 	</element>
 	<element name = "DelimitedRecord">
 		<annotation>
-			<documentation>Use this to construct a Delimited Record. (i.e. tab delimitted, comma delimitted, etc). At some point this will be expanded to include XYPlanes and RawImageFilePath.</documentation>
+			<documentation>Use this to construct a Delimited Record. (i.e. tab delimited, comma delimited, etc). At some point this will be expanded to include XYPlanes and RawImageFilePath.</documentation>
 		</annotation>
 		<complexType>
 			<sequence>
@@ -435,7 +435,7 @@ This means a stack statistics record that specifies theC as an index before theT
 			</attribute>
 			<attribute name = "RecordDelimiter" default = "\n" type = "string">
 				<annotation>
-					<documentation>This will be used to separate Records. Defaults to a newline (a newline as interpretted by perl).</documentation>
+					<documentation>This will be used to separate Records. Defaults to a newline (a newline as interpreted by perl).</documentation>
 				</annotation>
 			</attribute>
 		</complexType>
@@ -484,7 +484,7 @@ This means a stack statistics record that specifies theC as an index before theT
 		<annotation>
 			<documentation>Allows SemanticTypes Pixels and PixelsPlane to be outputs. The subelements specify locations for the population of data.
 This data population is useful for a Plane projection algorithm that has the same X and Y dimensions as the Pixels it is operating on.
-Alternately, these fields may be filled by ouput from STDOUT.
+Alternately, these fields may be filled by output from STDOUT.
 The FileSHA1 subelement is automatically calculated for the pixel dump file.
 			</documentation>
 		</annotation>

specification/src/main/resources/released-schema/2003-FC/MLI.xsd

@@ -82,7 +82,7 @@
 				<element name = "PixelsArray">
 					<annotation>
 						<documentation>Will pass a numeric matrix into the function.
-Translates a module input of Semantic Type Pixels (or any psuedo subclass of Pixels) to a numeric matrix. Limits specified by PixelsSlice or its subclasses will be honored.
+Translates a module input of Semantic Type Pixels (or any pseudo subclass of Pixels) to a numeric matrix. Limits specified by PixelsSlice or its subclasses will be honored.
 						</documentation>
 					</annotation>
 					<complexType>
@@ -126,7 +126,7 @@ In the future, can be used to establish references.
 					<complexType>
 						<attribute name = "InputLocation" use = "required" type = "string">
 							<annotation>
-								<documentation>Refers to a semantic element of a formal input. Syntax is formal input name, a period, and the semantic elment name. i.e. "Texture Direction.Direction_Value"</documentation>
+								<documentation>Refers to a semantic element of a formal input. Syntax is formal input name, a period, and the semantic element name. i.e. "Texture Direction.Direction_Value"</documentation>
 							</annotation>
 						</attribute>
 					</complexType>
@@ -139,7 +139,7 @@ In the future, can be used to establish references.
 			<choice>
 				<element name = "PixelsArray">
 					<annotation>
-						<documentation>Will translate a numeric array to a Formal Output of Semantic Type Pixels (or any psuedo subclass of Pixels). If PixelsSlice appears in the pseudo inheritance chain, the extents will be set to the extents of the Pixels.</documentation>
+						<documentation>Will translate a numeric array to a Formal Output of Semantic Type Pixels (or any pseudo subclass of Pixels). If PixelsSlice appears in the pseudo inheritance chain, the extents will be set to the extents of the Pixels.</documentation>
 					</annotation>
 					<complexType>
 						<attribute name = "FormalOutput" use = "required" type = "string">
@@ -157,7 +157,7 @@ In the future, can be used to stitch together data from different function outpu
 						<attribute name = "ConvertToDatatype">
 							<annotation>
 								<documentation>Useful when a function outputs a Pixels type that is unsupported by OME. The permitted list is the matlab types supported by OME.
-Note to perl developers: This list should stay syncronized with the Matlab Class to OME Type mapping hash $self->{ _matlab_class_to_pixel_type } that is defined in OME::Analysis::Handlers::MatlabHandler->new()
+Note to perl developers: This list should stay synchronized with the Matlab Class to OME Type mapping hash $self->{ _matlab_class_to_pixel_type } that is defined in OME::Analysis::Handlers::MatlabHandler->new()
 								</documentation>
 							</annotation>
 							<simpleType>
@@ -183,7 +183,7 @@ Note to perl developers: This list should stay syncronized with the Matlab Class
 						</attribute>
 						<attribute name = "OutputLocation" use = "required" type = "string">
 							<annotation>
-								<documentation>Refers to a semantic element of a formal output. Syntax is formal output name, a period, and the semantic elment name. i.e. "Angular Second Moment.ASM"</documentation>
+								<documentation>Refers to a semantic element of a formal output. Syntax is formal output name, a period, and the semantic element name. i.e. "Angular Second Moment.ASM"</documentation>
 							</annotation>
 						</attribute>
 					</complexType>
@@ -237,12 +237,12 @@ The contents of this element should follow CustomAttribute syntax and convention
 			<sequence>
 				<element name = "Element">
 					<annotation>
-						<documentation>Maps a location on the Vector to an output data location. Can be used in conjuction with Templates.</documentation>
+						<documentation>Maps a location on the Vector to an output data location. Can be used in conjunction with Templates.</documentation>
 					</annotation>
 					<complexType>
 						<attribute name = "OutputLocation" use = "required" type = "string">
 							<annotation>
-								<documentation>Refers to a semantic element of a formal output. Syntax is formal output name, a period, and the semantic elment name. i.e. "Angular Second Moment.ASM"</documentation>
+								<documentation>Refers to a semantic element of a formal output. Syntax is formal output name, a period, and the semantic element name. i.e. "Angular Second Moment.ASM"</documentation>
 							</annotation>
 						</attribute>
 						<attribute name = "Index" use = "required" type = "string">

specification/src/main/resources/released-schema/2003-FC/STD.xsd

@@ -82,7 +82,7 @@ to RC4 to reflect these changes.
 			<documentation>
 				Defines a semantic type.
 				Notes:
-				Granularity of SemanticType is infered from the granularity of the record it derives from. In a record, this granularity is specified by the AppliesTo attribute.
+				Granularity of SemanticType is inferred from the granularity of the record it derives from. In a record, this granularity is specified by the AppliesTo attribute.
 			</documentation>
 		</annotation>
 		<complexType>

specification/src/main/resources/released-schema/2003-FC/ome.xsd

@@ -59,7 +59,7 @@
 	<xs:element name = "OME">
 		<xs:annotation>
 			<xs:documentation>
-				The OME element is a container for all information objects acessible by OME.  These information objects include descriptions of the imaging experiments
+				The OME element is a container for all information objects accessible by OME.  These information objects include descriptions of the imaging experiments
 				and the people who perform them, descriptions of the microscope, the resulting images and how they were acquired, the analyses performed on those images,
 				and the analysis results themselves.
 				An OME file may contain any or all of this information.
@@ -288,7 +288,7 @@ is not specified, then the FIRST &lt;Pixels> element under &lt;Image> will be as
 				This element describes the type of experiment.  The required Type attribute must contain one or more entries from the following list:
 				FP FRET Time-lapse 4-D+ Screen Immunocytochemistry FISH Electrophysiology  Ion-Imaging Colocalization PGI/Documentation
 				FRAP Photoablation Optical-Trapping Photoactivation Fluorescence-Lifetime Spectral-Imaging Other
-				FP refers to fluorescent proteins, PGI/Docuemntation is not a 'data' image.
+				FP refers to fluorescent proteins, PGI/Documentation is not a 'data' image.
 				The optional Description element may contain free text to further describe the experiment.
 			</xs:documentation>
 		</xs:annotation>
@@ -1293,7 +1293,7 @@ is not specified, then the FIRST &lt;Pixels> element under &lt;Image> will be as
 			<xs:documentation>
 				The optical transfer function.  Filter ID refers to the set of filters used in computing the OTF.
 				BitsPerPixel is an integer '1', '8', '16'.
-				The OpticalAxisAvg is a boolean specifying wether or not optical axis averaging was done.
+				The OpticalAxisAvg is a boolean specifying whether or not optical axis averaging was done.
 				SizeX, SizeY specify the width and height of the OTF.
 				This element must contain a BinData element containing the Base64-encoded OTF.
 				Both of these work the same way as they do for the Data element within Image.
@@ -1319,7 +1319,7 @@ is not specified, then the FIRST &lt;Pixels> element under &lt;Image> will be as
 				Images can belong to more than one Dataset, and a Dataset may contain more than one Image.
 				Images contain one or more DatasetRef elements to specify what datasets they belong to.
 				Once a Dataset has been processed in any way, its collection of images cannot be altered.
-				Wether or not the list of Images in this dataset can be altered is specified by the Locked attribute.
+				Whether or not the list of Images in this dataset can be altered is specified by the Locked attribute.
 				The ExperimenterRef and GroupRef elements specify the person and group this Dataset belongs to.
 				Projects may contain one or more Datasets, and Datasets may belong to one or more Projects.
 				This relationship is specified by listing ProjectRef elements within the Dataset element.
@@ -1404,7 +1404,7 @@ is not specified, then the FIRST &lt;Pixels> element under &lt;Image> will be as
 			<xs:documentation>
 				Laser types are specified using two attributes - the Type and the lasing medium (Medium).  Type is a string which may be set to:
 				'Excimer','Gas','Metal Vapor','Solid State','Dye','Semiconductor', or 'Free Electron'.  The Medium attribute specifies the actual lasing medium
-				for a given laser type (for example, 'Nd-YAG').  Additionally, the Wavelength (in nm), wether or not the laser is FrequencyDoubled or Tunable may be specified.
+				for a given laser type (for example, 'Nd-YAG').  Additionally, the Wavelength (in nm), whether or not the laser is FrequencyDoubled or Tunable may be specified.
 				The Pulse attribute can be set to 'CW' (Continuous Wave),','Single','Q-Switched','Repetitive','Mode-Locked'.
 				The Power attribute specifies the nominal laser power in watts.
 				The Laser element may contain a Pump sub-element which refers to a LightSource used as a laser pump.