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/RadETL/R/radiologyProtocolConceptId_OccurrenceTable.R
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| a | b/RadETL/R/radiologyProtocolConceptId_OccurrenceTable.R | ||
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| 1 | #' 'radiologyProtocolConceptId' |
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| 2 | #' |
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| 3 | #' radiologyProtocolConceptId function indicates protocol&modality of each shoot |
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| 4 | #' |
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| 5 | #' |
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| 6 | #' @param DICOMList you can put it like this and then run the function : DICOMList<-DICOMHeaderList(DICOMFolderPath) |
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| 7 | #' @import dplyr |
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| 8 | #' @importFrom magrittr "%>%" |
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| 9 | #' |
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| 10 | #' |
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| 11 | #' @return A dataframe indicating path protocol&modality of each shoot |
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| 12 | #' @examples |
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| 13 | #' DICOMList<-DICOMHeaderList(DICOMFolderPath) |
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| 14 | #' radiologyProtocolConceptId(DICOMList) |
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| 15 | #' @export |
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| 16 | |||
| 17 | ##radiologyProtocolConceptId(BodyPartExamined, StudyDescription, radiologyPhaseConceptId, modality) |
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| 18 | |||
| 19 | radiologyProtocolConceptId<-function(DICOMList){ |
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| 20 | protocolName<-lapply(DICOMList, function(x){ |
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| 21 | protocolName<-as.character(x[[1]] %>% dplyr::filter(name %in% c('ProtocolName')) %>% dplyr::select(value)) |
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| 22 | if(protocolName=="character(0)" | protocolName==""){ |
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| 23 | protocolName='NA' |
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| 24 | } |
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| 25 | protocolName<-as.data.frame(protocolName) |
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| 26 | colnames(protocolName)<-'protocolName' |
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| 27 | return(protocolName)}) |
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| 28 | protocolName<-do.call(rbind,protocolName) |
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| 29 | information<-cbind(anatomicRegion(DICOMList), radiologyOccurrenceId(DICOMList), modalityImage(DICOMList), radiologyPhaseConceptId(DICOMList), imageOrientationConceptId(DICOMList), protocolName) |
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| 30 | information<-unique(information) |
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| 31 | information<-split(information, information$radiologyOccurrenceId) |
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| 32 | information<-lapply(information, function(x){ |
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| 33 | anatomicRegion<-data.frame(paste(unique(x$anatomicRegion), collapse=', '), row.names = NULL) |
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| 34 | colnames(anatomicRegion)<-'anatomicRegion' |
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| 35 | radiologyOccurrenceId<-data.frame(paste(unique(x$radiologyOccurrenceId), collapse=', '), row.names = NULL) |
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| 36 | colnames(radiologyOccurrenceId)<-'radiologyOccurrenceId' |
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| 37 | radiologyPhaseConceptId<-data.frame(paste(unique(x$radiologyPhaseConceptId), collapse=', '), row.names = NULL) |
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| 38 | colnames(radiologyPhaseConceptId)<-'radiologyPhaseConceptId' |
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| 39 | modality<-data.frame(paste(unique(x$modality), collapse=', '), row.names = NULL) |
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| 40 | colnames(modality)<-'modality' |
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| 41 | imageOrientationConceptId<-data.frame(paste(unique(x$imageOrientationConceptId), collapse=', '), row.names = NULL) |
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| 42 | colnames(imageOrientationConceptId)<-'imageOrientationConceptId' |
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| 43 | protocolName<-data.frame(paste(unique(x$protocolName), collapse=', '), row.names = NULL) |
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| 44 | colnames(protocolName)<-'protocolName' |
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| 45 | return(cbind(anatomicRegion, radiologyOccurrenceId, radiologyPhaseConceptId, modality, imageOrientationConceptId, protocolName))}) |
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| 46 | radiologyProtocolConceptId<-sapply(information, function(x){ |
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| 47 | if(grepl('chest', x$anatomicRegion)==T & grepl('DX', x$modality)==T & grepl('43591', x$imageOrientationConceptId)==T & grepl('43594', x$imageOrientationConceptId)==T){ |
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| 48 | return('3031526') |
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| 49 | } |
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| 50 | else if(grepl('chest', x$anatomicRegion)==T & grepl('CR', x$modality)==T & grepl('43591', x$imageOrientationConceptId)==T & grepl('43594', x$imageOrientationConceptId)==T){ |
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| 51 | return('3031526') |
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| 52 | } |
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| 53 | else if(grepl('chest', x$anatomicRegion)==T & grepl('DX', x$modality)==T & grepl('43594', x$imageOrientationConceptId)==T){ |
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| 54 | return('3002676') |
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| 55 | } |
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| 56 | else if(grepl('chest', x$anatomicRegion)==T & grepl('CR', x$modality)==T & grepl('43594', x$imageOrientationConceptId)==T){ |
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| 57 | return('3002676') |
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| 58 | } |
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| 59 | else if(grepl('head', x$anatomicRegion)==T & grepl('CT', x$modality)==T & grepl('5901', x$radiologyPhaseConceptId)==T){ |
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| 60 | return('36305291') |
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| 61 | } |
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| 62 | else if(grepl('head', x$anatomicRegion)==T & grepl('CT', x$modality)==T & grepl('28694', x$radiologyPhaseConceptId)==T){ |
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| 63 | return('3002086') |
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| 64 | } |
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| 65 | else if(grepl('head', x$anatomicRegion)==T & grepl('CT', x$modality)==T & grepl('28833', x$radiologyPhaseConceptId)==T){ |
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| 66 | return('3025779') |
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| 67 | } |
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| 68 | else if(grepl('neck', x$anatomicRegion)==T & grepl('CT', x$modality)==T & grepl('28694', x$radiologyPhaseConceptId)==T & grepl('angio', tolower(x$protocolName))==T){ |
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| 69 | return('36304600') |
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| 70 | } |
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| 71 | else if(grepl('abdomen', x$anatomicRegion)==T & grepl('CT', x$modality)==T & grepl('28833', x$radiologyPhaseConceptId)==T & grepl('11080', x$radiologyPhaseConceptId)==T & grepl('11085', x$radiologyPhaseConceptId)==T & grepl('11081', x$radiologyPhaseConceptId)==T){ |
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| 72 | return('21492176') |
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| 73 | } |
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| 74 | else if(grepl('abdomen', x$anatomicRegion)==T & grepl('CT', x$modality)==T & grepl('28694', x$radiologyPhaseConceptId)==T){ |
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| 75 | return('21492176') |
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| 76 | } |
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| 77 | else if(grepl('abdomen', x$anatomicRegion)==T & grepl('CR', x$modality)==T){ |
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| 78 | return('3053099') |
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| 79 | } |
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| 80 | else if(grepl('abdomen', x$anatomicRegion)==T & grepl('DX', x$modality)==T){ |
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| 81 | return('3053099') |
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| 82 | } |
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| 83 | else if(grepl('head', x$anatomicRegion)==T & grepl('MR', x$modality)==T){ |
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| 84 | return('3023655') |
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| 85 | } |
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| 86 | else { |
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| 87 | return('others') |
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| 88 | } |
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| 89 | }) |
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| 90 | radiologyProtocolConceptId<-data.frame(radiologyOccurrenceId=names(radiologyProtocolConceptId), radiologyProtocolConceptId=radiologyProtocolConceptId, row.names = NULL) |
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| 91 | return(radiologyProtocolConceptId) |
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| 92 | } |