Convert a gdt file and an image folder to a dicom file
License: GNU General Public License v3.0
ywesee Pharma Monitor
meteor npm i
meteor
Study Root not Patient Root. We could use the Patient ID as Study ID.sudo apt-get install dicom3toolsdciodvfy 2.dcmWarning - Missing attribute or value that would be needed to build DICOMDIR - Study Date
Warning - Missing attribute or value that would be needed to build DICOMDIR - Study Time
Warning - Missing attribute or value that would be needed to build DICOMDIR - Study ID
Warning - Missing attribute or value that would be needed to build DICOMDIR - Modality
Warning - Missing attribute or value that would be needed to build DICOMDIR - Series Number
Warning - Missing attribute or value that would be needed to build DICOMDIR - Instance Number
Warning - Value dubious for this VR - (0x0010,0x0010) PN Patient's Name PN [1] = <Hans Muster> - Retired Person Name form
MultiframeTrueColorSCImage
Error - Missing attribute Type 2C Conditional Element=<Laterality> Module=<GeneralSeries>
Look in current directory for directory names with 1-5 digits and recursively grab all jpgs in the folder and rename all jpgs with the 1-5 digit folder name in which the jpg was found. Save the renamed files in directory epat.
# Set the base directory
$baseDir = "C:\Users\zdava\Downloads\ul\ul\Convert"
# Output directory
$outputDir = "C:\Users\zdava\Downloads\ul\ul\Convert\epat"
# Create the output directory if it doesn't exist
if (-not (Test-Path -Path $outputDir)) {
New-Item -ItemType Directory -Path $outputDir | Out-Null
}
# Get subdirectories with names exactly 10 digits long
$subdirectories = Get-ChildItem -Path $baseDir -Directory | Where-Object { $_.Name -match '^\d{1,5}$' }
# Iterate through each subdirectory
foreach ($subdirectory in $subdirectories) {
# Get the 10-digit folder name
$folderName = $subdirectory.Name
# Get all JPG files in the current subdirectory and its subfolders
$jpgFiles = Get-ChildItem -Path $subdirectory.FullName -Recurse -Filter *.jpg
# Iterate through JPG files and rename them
foreach ($jpgFile in $jpgFiles) {
# Build the new filename
$newFilename = "{0}_{1}" -f $folderName, $jpgFile.Name
# Build the full path for the new file
$newFilePath = Join-Path -Path $outputDir -ChildPath $newFilename
# Move the file to the output directory with the new name
Move-Item -Path $jpgFile.FullName -Destination $newFilePath -Force
}
}
Write-Host "Files renamed and saved in epat directory!"
StoreSCP just doesn't care about the called aetitle and accepts whatever DICOM association comes in on it's listen port. Besides, aetitles would be a very poor mechanism for access control since they are user configurable.
dcmrecv.exe -d -aet echonas -od . 257
.\dicom2gdt.exe --dicom-file USm.1.2.840.113619.2.435.385968960.1709821542.73.1.512 --gdt-file .\gdt\ --jpegs .\jpgs\ dcmdump_ and the the DICOM unique ID.USECHONAS
PS C:\Users\zdava\Documents\gdt2dicom\gdt2dicom> cargo build
error: failed to select a version for `env_logger`.
... required by package `gdt2dicom v0.1.0 (C:\Users\zdava\Documents\gdt2dicom\gdt2dicom)`
versions that meet the requirements `^0.11.0` (locked to 0.11.0) are: 0.11.0
the package `gdt2dicom` depends on `env_logger`, with features: `anstream` but `env_logger` does not have these features.
It has an optional dependency with that name, but that dependency uses the "dep:" syntax in the features table, so it does not have an implicit feature with that name.
failed to select a version for `env_logger` which could resolve this conflict
gdt2dcm.wl.wlmscpfs (not part of gdt2dcm).wlmscpfs.exe -v -dfp C:\Users\medi-lan\gdt2dicom\dicom\medilan_MWL\ 107I: Association Received (SDS-SRV1:CorScribe -> medilan_MWL)
I: Refusing Association (bad application entity service)
You can test the worklist file using these steps:
dicommedilan_MWLmedilan_MWL called lockfiledump2dcm.exe .\wklist1.dump.txt .\wklist1.wl in the medilan_MWL dir.wlmscpfs.exe -v -dfp C:\Users\zdava\dicom\ 107
findscu -aet zeno -aec medilan_MWL -k "(0010,0010)=HEWETT*" localhost 107 do not confuse calling and called.gdt2dicom or dicom2gdt from github/tmp/target/release> ./dicom2gdt
./dicom2gdt: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by ./dicom2gdt)
./dicom2gdt: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by ./dicom2gdt)
./dicom2gdt: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by ./dicom2gdt)
/tmp/target/release> ./dicom2gdt
./dicom2gdt: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by ./dicom2gdt)
./dicom2gdt: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by ./dicom2gdt)
./dicom2gdt: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by ./dicom2gdt)
<?xml version="1.0" encoding="UTF-8"?>
<opp version="1.2">
<command type="UPDATE_CREATE" silent="NO"/>
<software name="My first PMS software App" version="1.0.0.1"/>
<patient reference="c19ea492ca35" firstName="John" lastName="Doe" birthdate="1992-03-31" gender="MALE">
</patient>
</opp>
Linux, Windows and MacOS
error: failed to select a version for `env_logger`.
... required by package `gdt2dicom v0.1.0 (/home/zeno/.software/gdt2dicom)`
versions that meet the requirements `^0.11.0` (locked to 0.11.0) are: 0.11.0
the package `gdt2dicom` depends on `env_logger`, with features: `anstream` but `env_logger` does not have these features.
It has an optional dependency with that name, but that dependency uses the "dep:" syntax in the features table, so it does not have an implicit feature with that name.
(0008,0018) has to be removed before running dump2dcm.(0008,0005) CS (no value available) # 0, 0 SpecificCharacterSet
(0008,0050) SH (no value available) # 0, 0 AccessionNumber
(0010,0010) PN [VIVALDI^ANTONIO] # 16, 1 PatientName
(0010,0020) LO [AV35674] # 8, 1 PatientID
(0010,0030) DA [16780304] # 8, 1 PatientBirthDate
(0010,0040) CS [M] # 2, 1 PatientSex
(0010,2000) LO (no value available) # 0, 0 MedicalAlerts
(0010,2110) LO (no value available) # 0, 0 Allergies
(0020,000d) UI [1.2.276.0.7230010.3.2.101] # 26, 1 StudyInstanceUID
(0032,1032) PN (no value available) # 0, 0 RequestingPhysician
(0032,1060) LO [holter] # 6, 1 RequestedProcedureDescription
(0040,0100) SQ (Sequence with explicit length #=1) # 50, 1 ScheduledProcedureStepSequence
(fffe,e000) na (Item with explicit length #=3) # 42, 1 Item
(0008,0060) CS [ECG] # 4, 1 Modality
(0040,0002) DA [20230530] # 8, 1 ScheduledProcedureStepStartDate
(0040,0003) TM [085607] # 6, 1 ScheduledProcedureStepStartTime
(fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem
# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 148 # 4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion
(0002,0002) UI =MultiframeGrayscaleByteSecondaryCaptureImageStorage # 28, 1 MediaStorageSOPClassUID
(0002,0003) UI (no value available) # 0, 0 MediaStorageSOPInstanceUID
(0002,0010) UI =JPEGBaseline # 22, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.7] # 28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_367] # 16, 1 ImplementationVersionName
# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 198 # 4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion
(0002,0002) UI [1.2.276.0.7230010.3.1.0.1] # 26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.2.276.0.7230010.3.1.4.3284257161.7184.1685536943.349] # 54, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianExplicit # 20, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.7] # 28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_367] # 16, 1 ImplementationVersionName
xml2dcm creates "strange" headers.dump2dcm creates the right headers. But I do not know what happens if you first run xml2dcmdump2dcm will create different headers for the .wl file.VDDS_MMI.ini for the parameters.VDDS_MMI.ini for the parameters. Sample of a VDDS_MMI.ini.txt the [BFS] tag can be ignored, it is being used for the "Befund".NAME1=orangedental_byzzStufe 1: Die PVS ruft das Importmodul der BVS zur Übergabe der Patientendaten auf.Stufe 3: Die PVS ruft das Modul zum Export der Bildinformationen der BVS auf.gdt2dicom_PVS. That we will have to write into VDDS_MMI.ini on the system.PatientTransfer.ini we can also specify where we want the JPEG files to be saved after the scan has been done. (chapter 3.2) MMOINFEXPORT, MMOINFEXPORT_OSc:\program files\byzz nxt\byzz.Vdds.exe PatientTransfer.inigdt2vdds$folderPath = "S:\GDT-PhysioPort"
$fileName = "epat.gdt"
$newFileName = "vitaepat.gdt"
while ($true) {
# Check if the file exists in the specified folder
if (Test-Path (Join-Path $folderPath $fileName)) {
# Rename the file
Rename-Item (Join-Path $folderPath $fileName) (Join-Path $folderPath $newFileName)
Write-Host "File '$fileName' found and renamed to '$newFileName'."
}
# Wait for 5 seconds before checking again
Start-Sleep -Seconds 5
}
dcmodify -i "0008,0060=ECG" test.dcmdcmodify -i "0032,1060=holter" test.dcmgdt2dicom --gdt-file epat.gdt --output epat.wlgdt2dicom --gdt-file epat.gdt --tag 0008,0060=ECG,0032,1060=holter --output epat.wlMortara Hscribe is pretty fussy about the Worklist files. They really have to be in the right format.
H-Scribe and X-Scribe DICOM Conformance Statement.pdf
1.dcm.txt
2.dcm.txt
3.dcm.txt
hscribe_manual.pdf
Starterpaket) file standard is widely used in Germany, but it does not contain image information.img2dcm. img2dcm software converts JPEGs to DICOM files. img2dcm also takes XML as input.dcmdump of dcmtk tools will show you all the contents of a dicom file.dcm2xml.dtd will show you the valid XML that img2dcm can take as input. The GDT file has to be converted into valid DICOM XML according to dcm2xml.dtd.dcm2xml is also part of the dcmtk toolkit.worklist_server.ps1
$command = 'wlmscpfs.exe -v -d -dfr -dfp C:\Users\medi-lan\gdt2dicom\dicom\ 256'
Start-Process -FilePath "cmd.exe" -ArgumentList "/c `"$command`"" -WindowStyle Hidden
check if the worklist is running: tasklist.exe | findstr wlmscpfs
start_gdt2ws.ps1 -> #19 (comment)
while ($true) {
# Run the command
& "C:\Users\medi-lan\gdt2dicom\gdt2ws.ps1"
# Pause for 10 seconds
Start-Sleep -Seconds 10
}
gdt2dicom without image input Dir?.\gdt2vdds.exe --gdt-file .\gdt\ --output .\jpeg2epat\ --bvs 3Shape[2024-03-01T11:21:51Z INFO gdt2vdds] Loading VDDS_MMI: C:\Windows\VDDS_MMI.INI
thread 'main' panicked at src\bin\gdt2vdds.rs:72:52:
called `Option::unwrap()` on a `None` value
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
$directory = 'C:\Users\medi-lan\gdt2dicom\gdt'
$originalFileName = 'epat.gdt'
# Check if the file exists in the directory
$files = Get-ChildItem -Path $directory -Filter $originalFileName
if ($files.Count -gt 0) {
$timestamp = Get-Date -Format 'yyyyMMddHHmmss'
$counter = 1
foreach ($file in $files) {
$extension = $file.Extension
$newName = "$timestamp" + "_epat_$counter" + $extension
$newPath = Join-Path -Path $directory -ChildPath $newName
Rename-Item -Path $file.FullName -NewName $newPath
$counter++
}
Write-Host "Files renamed successfully."
} else {
Write-Host "No files named '$originalFileName' found in the directory."
}
$gdtDirectory = 'C:\Users\medi-lan\gdt2dicom\gdt'
$outputDirectory = 'C:\Users\medi-lan\gdt2dicom\wl'
$gdt2dicomExe = 'C:\Users\medi-lan\gdt2dicom\gdt2dicom.exe'
# Create the output directory if it doesn't exist
if (-not (Test-Path -Path $outputDirectory)) {
New-Item -ItemType Directory -Path $outputDirectory | Out-Null
}
# Get all GDT files in the input directory
$gdtFiles = Get-ChildItem -Path $gdtDirectory -Filter '*.gdt'
foreach ($gdtFile in $gdtFiles) {
$outputFile = Join-Path -Path $outputDirectory -ChildPath ($gdtFile.Name -replace '\.gdt$', '.wl')
& $gdt2dicomExe --gdt-file $gdtFile.FullName --output $outputFile
}
Powershell script to map file names of all files in a directory against a text file. UID of the filename has to updated if last name and first name match with the txt file. The format of the file name and the format of every line in the txt file are the same: After the first two __ comes the uid, after the thrid _ comes the last name and after the fourth _ comes the first name
# Set the paths for the input directory, text file, and output directory
$inputDirectory = "C:\Users\medi-lan\Documents\gdt2dicom\wrong_patient_id"
$textFilePath = "C:\Users\medi-lan\Documents\gdt2dicom\plist.txt"
$outputDirectory = "C:\Users\medi-lan\Documents\gdt2dicom\new_file_name"
# Create the output directory if it doesn't exist
if (-not (Test-Path -Path $outputDirectory)) {
New-Item -ItemType Directory -Path $outputDirectory | Out-Null
}
# Read the content of the text file into a hashtable for quick lookup
$uidLookup = @{}
Get-Content -Path $textFilePath | ForEach-Object {
$parts = $_ -split '_'
$uid = $parts[2]
$lastName = $parts[3]
$firstName = $parts[4]
$key = "$lastName,$firstName"
$uidLookup[$key] = $uid
}
# Process files in the input directory
Get-ChildItem -Path $inputDirectory | ForEach-Object {
if ($_.PSIsContainer -eq $false) {
# Extract information from the file name
$fileNameParts = $_.BaseName -split '_'
$uid = $fileNameParts[2]
$lastName = $fileNameParts[3]
$firstName = $fileNameParts[4]
# Check if there is a matching UID in the text file
$key = "$lastName,$firstName"
if ($uidLookup.ContainsKey($key)) {
$uid = $uidLookup[$key]
# Construct the new file name without "H__" and with ".pdf" extension
$newFileName = "{1}_{2}_{3}_{4}.pdf" -f $fileNameParts[0], $fileNameParts[1], $uid, $lastName, $firstName
# Build the full output path
$outputPath = Join-Path -Path $outputDirectory -ChildPath $newFileName
# Copy the file with the updated filename to the output directory
Copy-Item -Path $_.FullName -Destination $outputPath
}
}
}
$files = Get-ChildItem -Path $outputDirectory
# Iterate through each file
foreach ($file in $files) {
# Construct the new file name by removing underscores at the beginning
$newFileName = $file.Name -replace '^_+'
# Create the new file path
$newFilePath = Join-Path -Path $outputDirectory -ChildPath $newFileName
# Rename the file
Rename-Item -Path $file.FullName -NewName $newFileName -Force
}
Write-Host "Underscores at the beginning of file names have been removed."
Write-Host "Script execution completed."
Aplio A Pflichtfelder
(0008,0050) AccessionNumber
(0010,0010) PatientName
(0010,0020) PatientiD
(0020,000D) StudyinstanceUID
(0032,1060) RequestedProcedureDescription
(0040,0100) ScheduledProcedureStepSequence
ITEM 1|
(0008,0060) Modality
(0040,0001) ScheduledStationAETitle
(0040,0002) ScheduledProcedureStepStartDate
(0040,0003) ScheduledProcedureStepStartTime
(0040,0007) ScheduledProcedureStepDescription
(0040,0009) ScheduledProcedureStepID
ITEM 2
(0040,1001) RequestedProcedurelD
./target/debug/gdt2dicom --gdt-file epat.gdt --jpegs 1 --output /tmp/1.dcmError: Os { code: 2, kind: NotFound, message: "No such file or directory" }Line 40 in e95bb28
According to the PDF specifications it should be MMDDYYYY
dicom2gdt binary.dicom2gdt should convert a DICOM file to a GDT file, including the images and all the data about the patient from the DICOM file. Output files should be jpeg.dcmj2pnm --write-jpeg 1.dcm ./output --all-frames will write jpeg files.With timestamp
# Specify input and output directories
$inputDir = "C:\Path\To\Input\Directory"
$outputDir = "C:\Path\To\Output\Directory"
# Get all DICOM files in the specified directory
$dicomFiles = Get-ChildItem -Path $inputDir -Filter *
foreach ($file in $dicomFiles) {
# Use dcmdump to extract the DICOM tags
$tags = & "dcmdump.exe" $file.FullName | Select-String -Pattern "(0010,0020|0010,0010|05af,0010)"
# Extract values in between square brackets []
$tagValues = $tags -replace '[^\[\]]*\[([^\[\]]*)\][^\[\]]*', '$1'
# Ensure "0010,0020" is in the first position
$sortedTagValues = $tagValues | Sort-Object {$_ -eq '0010,0020'} -Descending
# Create a timestamp in the format YYYYMMDD_HHMMSS
$timestamp = Get-Date -Format "yyyyMMdd_HHmmss"
# Create a new filename based on the extracted values and timestamp
$newFilename = "$($sortedTagValues -join '_')_$timestamp.dcm"
# Construct the full path for the output file
$outputPath = Join-Path -Path $outputDir -ChildPath $newFilename
# Read the content of the original file as bytes
$fileContent = [System.IO.File]::ReadAllBytes($file.FullName)
# Write the content to the new file in the output directory
[System.IO.File]::WriteAllBytes($outputPath, $fileContent)
Write-Host "Copied and renamed $($file.FullName) to $outputPath"
}
Without timestamp
# Specify input and output directories
$inputDir = "C:\Path\To\Input\Directory"
$outputDir = "C:\Path\To\Output\Directory"
# Get all DICOM files in the specified directory
$dicomFiles = Get-ChildItem -Path $inputDir -Filter *
foreach ($file in $dicomFiles) {
# Use dcmdump to extract the DICOM tags
$tags = & "dcmdump.exe" $file.FullName | Select-String -Pattern "(0010,0020|0010,0010|05af,0010)"
# Extract values in between square brackets []
$tagValues = $tags -replace '[^\[\]]*\[([^\[\]]*)\][^\[\]]*', '$1'
# Ensure "0010,0020" is in the first position
$sortedTagValues = $tagValues | Sort-Object {$_ -eq '0010,0020'} -Descending
# Create a new filename based on the extracted values
$newFilename = "$($sortedTagValues -join '_').dcm"
# Construct the full path for the output file
$outputPath = Join-Path -Path $outputDir -ChildPath $newFilename
# Read the content of the original file as bytes
$fileContent = [System.IO.File]::ReadAllBytes($file.FullName)
# Write the content to the new file in the output directory
[System.IO.File]::WriteAllBytes($outputPath, $fileContent)
Write-Host "Copied and renamed $($file.FullName) to $outputPath"
}
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