Merge pull request #231 from Emory-HITI/dev

Create the MRI SUVPaR module

modules/rta-extraction/README.md

@@ -4,20 +4,23 @@ The RTA Extractor runs continuously to load the data (labs, meds and orders) in
 
 # Configuring Niffler RTA Extractor
 
-Niffler real-time extraction must be configured as a service for it to run continuously and resume automatically even when the server restarts. Unless you are the administrator who is configuring Niffler for the first time, skip this section.
+Niffler RTA Extractor must be configured as a service for it to run continuously and resume automatically even when the server restarts. Unless you are the administrator who is configuring Niffler for the first time, skip this section.
 
 Find the system.json file in the service folder and modify accordingly.
 
 system.json entries are to be set *only once* for the Niffler deployment by the administrator. Once set, further extractions do not require a change.
 
-* *DCM4CHEBin*: Set the correct location of the DCM4_CHE folder.
-
-* *QueryAet*: Set the correct AET:PORT of the querying AET (i.e., this script). Typically same as the values you set for the storescp.
-
-* *StorageFolder*: Create a folder where you like your DICOM files to be. Usually, this is an empty folder (since each extraction is unique). 
-
-* *FilePath*: By default, "{00100020}/{0020000D}/{0020000E}/{00080018}.dcm". This indicates a hierarchical storage of patients/studies/series/instances.dcm. Leave this value as it is unless you want to change the hierarchy.
-
+ * *LabsURL*: Set the URL providing continous labs data.
+ * *MedsURL*: Set the URL providing continous meds data.
+ * *OrdersURL*: Set the URL providing continous orders data.
+ * *LabsDataLoadFrequency*: Time Frequency for loading labs data onto MongoDB. The frequency is to be provided in minutes.
+ * *MedsDataLoadFrequency*: Time Frequency for loading meds data onto MongoDB. The frequency is to be provided in minutes.
+ * *OrdersDataLoadFrequency*: Time Frequency for loading orders data onto MongoDB. The frequency is to be provided in minutes.
+ * *UserName*: Set the Username Credentials for RTA Connection.
+ * *PassCode*: Set the Passcode Credentials for RTA Connection.
+ * *MongoURI*: Set the MongoDB Connection URL.
+ * *MongoUserName*: Set the MongoDB Username for Credentials.
+ * *MongoPassCode*: Set the MongoDB Passcode for Credentials.
 
 ## Configure DICOM attributes to extract
 

modules/suvpar/README.md

@@ -0,0 +1,24 @@
+# SUVPaR: Scanner Usage Visualization with PACS and RIS data
+
+This is a module that utilizes Niffler's other modules and [Eaglescope](https://github.com/sharmalab/eaglescope) to 
+visualize MRI Scanner Usage.
+
+
+# Configuring Niffler SUVPaR
+
+Find the config.json file in the folder and modify accordingly.
+
+* *InputFile*: The metadata in a csv file, as produced by the cold-extraction -> png-extraction workflow.
+
+* *OutputFile*: The output csv file with just the properties listed in the FeaturesetFile.
+
+* *FeaturesetFile*: The subset of the properties that must be stored in the OutputFile.
+
+
+# Running Niffler SUVPaR
+
+First, to run the script to trim the file.
+
+````
+$ python3 Strip.py
+````

modules/suvpar/Strip.py

@@ -0,0 +1,25 @@
+import pandas
+import logging
+import json
+
+logging.basicConfig(level=logging.INFO)
+
+
+def initialize_config_and_execute():
+    with open('config.json', 'r') as f:
+        config = json.load(f)
+
+    feature_file = config['FeaturesetFile']
+    filename = config['InputFile']
+    output_csv = config['OutputFile']
+
+    text_file = open(feature_file, "r")
+    feature_list = text_file.read().split('\n')
+
+    filtered_csv = pandas.read_csv(filename, usecols=lambda x: x in feature_list, sep=',')
+    df = pandas.DataFrame(filtered_csv)
+    df.to_csv(output_csv)
+
+
+if __name__ == "__main__":
+    initialize_config_and_execute()

modules/suvpar/config.json

@@ -0,0 +1,6 @@
+{
+  "InputFile": "sample.csv",
+  "OutputFile": "output.csv",
+  "FeaturesetFile": "featureset.txt"
+
+}

modules/suvpar/featureset.txt

@@ -0,0 +1,47 @@
+AccessionNumber
+InstitutionAddress
+PatientSex
+StudyDate
+StudyTime
+DeviceSerialNumber
+PatientID
+StudyDescription
+ProtocolName
+PerformedProcedureStepDescription
+NumberOfStudyRelatedSeries
+NumberOfStudyRelatedInstances
+AcquisitionDate
+AcquisitionTime
+SeriesDate
+SeriesTime
+SeriesNumber
+SeriesDescription
+ImageType
+SequenceName
+MRAcquisitionType
+ScanOptions
+ReceiveCoilName
+ImagesInAcquisition
+InstanceNumber
+AcquisitionDuration
+ReconstructionDiameter
+PercentPhaseFieldOfView
+PixelSpacing
+AcquisitionMatrix
+InPlanePhaseEncodingDirection
+SliceThickness
+RepetitionTime
+EchoTime
+InversionTime
+NumberOfAverages
+EchoNumbers
+SpacingBetweenSlices
+NumberOfPhaseEncodingSteps
+EchoTrainLength
+PercentSampling
+PixelBandwidth
+FlipAngle
+SAR
+Modality
+Manufacturer
+ManufacturerModelName

modules/suvpar/sample.csv

@@ -0,0 +1,4 @@
+PatientID,PatientName,PatientSex
+1,AAA,F
+2,BBB,M
+3,CCC,F