Public Member Functions | |
| LIDCNodule () | |
| Create a new, blank nodule structure. | |
| LIDCNodule (XmlElement el) | |
| Create a nodule structure from an XML element. | |
| LIDCNodule (int[,] originalPixelData, int minX, int maxX, int minY, int maxY) | |
| Create a nodule structure from raw original pixel data. | |
| void | FromXML (XmlElement el) |
| Read nodule data from an XML element. | |
| XmlElement | ToXML (XmlDocument doc) |
| Save nodule data to an XML element. | |
| bool | Equals (LIDCNodule n) |
| Compares two LIDCNodule objects. | |
| void | Merge (LIDCNodule n) |
| Merges in secondary data from another node that doesn't exist in this node. | |
| string | GetSegmentedDICOMFilename () |
| Builds the filename of the corresponding DICOM segmented nodule image. | |
| string | GetOriginalDICOMFilename () |
| Builds the filename of the corresponding original DICOM image. | |
| PhysicalSize | GetActualSize () |
| Reads the DICOM pixel spacing property and calculates the nodule's actual height and width in millimeters. | |
| void | CalculateCentroid () |
| Calculate the nodule centroid (point data must be loaded). | |
| void | PurgePixelData () |
| De-allocate pixel data from memory. | |
Public Attributes | |
| int | NUID |
| Unique nodule ID (assigned in constructor -- will NEVER be the same for two different LIDCNodule objects!). | |
| string | MdbPK |
| Primary key value from Ekarin's Access database file (not used - DEPRECATED). | |
| string | StudyInstanceUID |
| Study ID number from DICOM files. | |
| string | SeriesInstanceUID |
| Series ID number from DICOM files. | |
| string | NoduleID |
| Nodule ID number from XML annotation (unique nodule, physician, series). | |
| string | Nodule_no |
| Nodule number -- identifies the same nodule from different slices and/or physicians (computed by Ekarin using centroid comparison). | |
| string | ImageSOP_UID |
| Image ID number from DICOM files. | |
| int | MinX |
| Left boundary of nodule with respect to the original DICOM file dimensions. | |
| int | MaxX |
| Right boundary of nodule with respect to the original DICOM file dimensions. | |
| int | MinY |
| Top boundary of nodule with respect to the original DICOM file dimensions. | |
| int | MaxY |
| Bottom boundary of nodule with respect to the original DICOM file dimensions. | |
| string | Slice |
| CT slice number (last number in imageSOP_UID). | |
| int | CentroidX |
| X-coordinate of nodule centroid. | |
| int | CentroidY |
| Y-coordinate of nodule centroid. | |
| int | Width |
| Nodule width (maxX - minX) in pixels. | |
| int | Height |
| Nodule height (maxY - minY) in pixels. | |
| double | ActualWidth = double.NaN |
| Physical width in millimeters. | |
| double | ActualHeight = double.NaN |
| Physical height in millimeters. | |
| double | Temp_dist |
| Temporary variable used for storing distance from query images while running a query. | |
| double | Temp_adist |
| Temporary variable used for storing annotation distance from query images while running a query. | |
| Dictionary< string, double > | Haralick |
| Haralick data as dictionary with feature name-value pairs. | |
Properties | |
| double[,][] | GaborHist [get, set] |
| Accessor for gaborHist. Can re-bin histogram based on public field GaborHistDivBy. | |
| int | gaborHistDivBy = 0 [] |
| How much to divide the histogram by. | |
| int | GaborHistDivBy [get, set] |
| Accessor for gaborHistDivBy. Verifies that the value is a power of two. | |
| double[,] | GaborMean = null [] |
| Mean Gabor response. | |
| double[,] | GaborStdDev = null [] |
| Standard deviation of Gabor responses. | |
| double[][] | markovHist = null [] |
| Markov data. | |
| double[][] | markovHistResized = null [] |
| Resized histogram. It is here for optimization. Since we will probably access the histogram multiple times before resizing it, there is no need to recompute it each time -- just store it in here. | |
| double[][] | MarkovHist [get, set] |
| Accessor for the Markov histogram. Used to resize the histogram. | |
| int | markovHistDivBy = 0 [] |
| How much to divide the histogram by. | |
| int | MarkovHistDivBy [get, set] |
| Accessor for the Markov histogram divisor. | |
| double[] | MarkovMean = null [] |
| Mean of the Markov data. | |
| double[] | MarkovStd = null [] |
| Standard deviation of the Markov data. | |
| Dictionary< string, int > | Annotations [] |
| Annotation data as dictionary with annotation name-value pairs. | |
| List< Point > | Points [] |
| Nodule contour data as list of points. | |
| int[,] | segmentedPixelData [] |
| Raw DICOM pixel data (segmented - pixels outside the boundary contain the value Util.BG_VALUE). | |
| int[,] | originalPixelData [] |
| Raw DICOM pixel data (full image). | |
| string | OriginalDICOMFilename [] |
| Filename (relative to Util.DATA_PATH) for original DICOM image. | |
| int[,] | SegmentedPixelData [get] |
| Returns the extracted DICOM pixel data (pixels outside the boundary contain the value Util.BG_VALUE). | |
| int[,] | OriginalPixelData [get] |
| Returns the original DICOM pixel data. | |
| static bool | SAVE_XML_PRIMARY = true [] |
| Whether to save primary data (series, noduleID, etc.) when exporting to XML. | |
| static bool | SAVE_XML_BOUNDS = false [] |
| Whether to save min/max pixel boundary data when exporting to XML. | |
| static bool | SAVE_XML_ANNOTATIONS = false [] |
| Whether to save annotation data when exporting to XML. | |
| static bool | SAVE_XML_HARALICK = false [] |
| Whether to save haralick data when exporting to XML. | |
| static bool | SAVE_XML_GABOR = false [] |
| Whether to save Gabor data when exporting to XML. | |
| static bool | SAVE_XML_MARKOV = false [] |
| Whether to save Markov data when exporting to XML. | |
| static bool | SAVE_XML_POINTS = false [] |
| Whether to save point data when exporting to XML. | |
Private Member Functions | |
| double[,][] | getSmallGaborHist (int divBy) |
| Bins the Gabor histogram in to a smaller histogram. | |
| double[][] | getSmallMarkovHist (int divBy) |
| Bins the Markov histogram in to a smaller histogram. | |
| string | getXMLTextElement (XmlElement el, string name) |
| Reads a value from an XML element. | |
| XmlElement | createXMLTextElement (XmlDocument doc, string name, string value) |
| Generates an XML element object with the specified subelement. | |
Private Attributes | |
| double[,][] | gaborHist = null |
| Two dimensional array of Gabor response histograms (orientation x scale). | |
| double[,][] | gaborHistResized = null |
| Resized histogram. It is here for optimization. Since we will probably access the histogram multiple times before resizing it, there is no need to recompute it each time -- just store it in here. | |
Static Private Attributes | |
| static int | nextNUID = 0 |
| Used to assign each nodule a unique number. | |
Classes | |
| struct | PhysicalSize |
| Structure for representing the physical size of a nodule. More... | |
| BRISC::Core::LIDCNodule::LIDCNodule | ( | XmlElement | el | ) | [inline] |
Create a nodule structure from an XML element.
| el | Element to parse |
| BRISC::Core::LIDCNodule::LIDCNodule | ( | int | originalPixelData[,], | |
| int | minX, | |||
| int | maxX, | |||
| int | minY, | |||
| int | maxY | |||
| ) | [inline] |
Create a nodule structure from raw original pixel data.
| originalPixelData | Two-dimensional integer pixel data | |
| minX | Left boundary | |
| maxX | Right boundary | |
| minY | Top boundary | |
| maxY | Bottom boundary |
| XmlElement BRISC::Core::LIDCNodule::createXMLTextElement | ( | XmlDocument | doc, | |
| string | name, | |||
| string | value | |||
| ) | [inline, private] |
Generates an XML element object with the specified subelement.
| doc | Target XML document | |
| name | Desired element name | |
| value | Desired element value |
| bool BRISC::Core::LIDCNodule::Equals | ( | LIDCNodule | n | ) | [inline] |
Compares two LIDCNodule objects.
| n | Comparison nodule |
| void BRISC::Core::LIDCNodule::FromXML | ( | XmlElement | el | ) | [inline] |
Read nodule data from an XML element.
| el | Element to parse |
| PhysicalSize BRISC::Core::LIDCNodule::GetActualSize | ( | ) | [inline] |
Reads the DICOM pixel spacing property and calculates the nodule's actual height and width in millimeters.
| string BRISC::Core::LIDCNodule::GetOriginalDICOMFilename | ( | ) | [inline] |
Builds the filename of the corresponding original DICOM image.
| string BRISC::Core::LIDCNodule::GetSegmentedDICOMFilename | ( | ) | [inline] |
Builds the filename of the corresponding DICOM segmented nodule image.
| double [,][] BRISC::Core::LIDCNodule::getSmallGaborHist | ( | int | divBy | ) | [inline, private] |
Bins the Gabor histogram in to a smaller histogram.
| divBy | Number to divide the origional histogram by. Must be a power of two, anything else returns null |
| double [][] BRISC::Core::LIDCNodule::getSmallMarkovHist | ( | int | divBy | ) | [inline, private] |
Bins the Markov histogram in to a smaller histogram.
| divBy | Number to divide the origional histogram by. Must be a power of two, anything else returns null |
| string BRISC::Core::LIDCNodule::getXMLTextElement | ( | XmlElement | el, | |
| string | name | |||
| ) | [inline, private] |
Reads a value from an XML element.
| el | Parent XML element to read | |
| name | Name of desired element |
| void BRISC::Core::LIDCNodule::Merge | ( | LIDCNodule | n | ) | [inline] |
Merges in secondary data from another node that doesn't exist in this node.
| n | Node with additional data |
| XmlElement BRISC::Core::LIDCNodule::ToXML | ( | XmlDocument | doc | ) | [inline] |
Save nodule data to an XML element.
| doc | Target XML document |
1.4.7