Additions to hdr module.

.gitignore

@@ -96,3 +96,9 @@ ENV/
 
 # vscode
 settings.json
+
+# PyCharm
+.idea/
+
+# Custom
+scratch/

ifcb/data/hdr.py

@@ -1,21 +1,21 @@
 """
 Support for parsing IFCB header files.
 """
-
-import re
-import fileinput
-
 import ast
+import fileinput
+from os import PathLike
+import re
+import yaml
 
-HDR='hdr'
+HDR = 'hdr'
 
 # hdr attributes. these are camel-case, mapped to column names below
 TEMPERATURE = 'temperature'
 HUMIDITY = 'humidity'
 BINARIZE_THRESHOLD = 'binarizeThreshold'
 SCATTERING_PMT_SETTING = 'scatteringPhotomultiplierSetting'
 FLUORESCENCE_PMT_SETTING = 'fluorescencePhotomultiplierSetting'
-BLOB_SIZE_THRESHOLD = 'blobSizeThreshold' 
+BLOB_SIZE_THRESHOLD = 'blobSizeThreshold'
 
 # column name / type pairs
 HDR_SCHEMA = [(TEMPERATURE, float),
@@ -29,7 +29,8 @@
 
 CONTEXT = 'context'
 
-def parse_alt_header(lines):
+
+def parse_alt_header(lines: list) -> dict:
     props = {}
     for line in lines:
         m = re.match(r'^run time = ([\d.]+) s\s+inhibit time = ([\d.]+)', line)
@@ -43,7 +44,8 @@ def parse_alt_header(lines):
             props['humidity'] = float(m.group(2))
     return props
 
-def parse_hdr(lines):
+
+def parse_hdr(lines: list) -> dict:
     """
     Given the lines of a header file, return the properties in it.
 
@@ -56,12 +58,12 @@ def parse_hdr(lines):
     if lines[0] == 'Imaging FlowCytobot Acquisition Software version 2.0; May 2010':
         if lines[1].startswith('Sample Date'):
             return parse_alt_header(lines)
-        props = { CONTEXT: lines[0] } # FIXME parse
-    elif re.match(r'^[Ss]oftwareVersion:',lines[0]):
-        props = { CONTEXT: lines[0] }
+        props = {CONTEXT: lines[0]}  # FIXME parse
+    elif re.match(r'^[Ss]oftwareVersion:', lines[0]):
+        props = {CONTEXT: lines[0]}
         for line in lines[1:]:
             try:
-                k, v = re.split(r': ',line)
+                k, v = re.split(r': ', line)
                 try:
                     v = ast.literal_eval(v)
                 except ValueError:
@@ -74,11 +76,11 @@ def parse_hdr(lines):
                 pass
     else:
         # "context" is what the text on lines 2-4 is called in the header file
-        props = { CONTEXT: '\n'.join([line.strip('"') for line in lines[:-2]]) }
+        props = {CONTEXT: '\n'.join([line.strip('"') for line in lines[:-2]])}
         # now handle format variants
-        if len(lines) >= 6: # don't fail on original header format
-            columns = re.split(' +',re.sub('"','',lines[-2])) # columns of metadata in CSV format
-            values = re.split(' +',re.sub(r'[",]',' ',lines[-1]).strip()) # values of those columns in CSV format
+        if len(lines) >= 6:  # don't fail on original header format
+            columns = re.split(' +', re.sub('"', '', lines[-2]))  # columns of metadata in CSV format
+            values = re.split(' +', re.sub(r'[",]', ' ', lines[-1]).strip())  # values of those columns in CSV format
             # for each column take the string and cast it to the schema's column type
             for (column, (name, _), value) in zip(HDR_COLUMNS, HDR_SCHEMA, values):
                 props[name] = value
@@ -88,7 +90,37 @@ def parse_hdr(lines):
             props[name] = cast(props[name])
     return props
 
-def parse_hdr_file(path):
+
+def _get_software_version(hdr_filepath: PathLike) -> str:
+    """
+    Return the software version that is within an IFCB .hdr file.
+
+    :param hdr_filepath: A path-like string to the .hdr file.
+    :return: The software version as a string. Typically, in the format of N.N.N.N representing major.minor.patch.build.
+    """
+    with open(hdr_filepath, 'r') as _file:
+        lines = _file.readlines()
+    for line in lines:
+        if 'software' in line.lower():
+            version = re.findall(r'([0-9.]+)', line)[0]
+            return version
+    raise IOError(f"Software version information not found in header: {hdr_filepath}")
+
+
+def _parse_hdr(hdr_filepath: PathLike) -> dict:
+    """
+    Parse a .hdr file as YAML.
+
+    :param hdr_filepath: A path-like string to the .hdr file.
+    :returns dict: A dictionary containing the parsed header data.
+    """
+
+    with open(hdr_filepath, 'r') as _file:
+        hdr_data = yaml.safe_load(_file)
+    return hdr_data
+
+
+def parse_hdr_file(path: PathLike) -> dict:
     """
     Given a path to a header file, return the header properties.
 

ifcb/tests/test_files/D20190929T185847_IFCB122.hdr

@@ -0,0 +1,134 @@
+softwareVersion: Imaging FlowCytobot Acquisition Software version 1.1.5.19
+HousekeepingFirmwareVersion: 32
+AnalogFirmwareVersion: 45
+SyringeNumber: 1
+sampleTime: 2019-09-29T18:58:47Z
+imagerID: 122
+KloehnPort: COM3
+DataFilePath: C:\Data\Kavanaugh_Shimada_Sep2019\
+syringeOffset: 5437
+appDebug: 1
+viewImages: 0
+blobAnalysis: 1
+pumpDriveBoardPresent: 0
+backflushWithSample: 0
+outputFiles: 1
+fluidicsVerbose: 0
+fluidsActive: 1
+binarizeThreshold: 5
+blobXgrowAmount: 20
+imageResizeFactor: 8
+minimumBlobArea: 1500
+triggerPulseEndtoADCstart_x2170ns_DAQ_MCC_only: 8
+PMTAhighVoltage: 0.550000
+PMTBhighVoltage: 0.700000
+PMTChighVoltage: 0.000000
+DAQ_MCCserialPort_DAC_MCConly: COM1
+ADCdataRateDAQ_MCConly: 240
+FlashlampControlVoltage: 2.400000
+FanTemperatureThreshold_DAC_MCConly: 117964
+FanTemperatureHysteresis_DAC_MCConly: 123
+ValveHumidityThreshold_DAC_MCConly: 65621
+ValveHumidityHysteresis_DAC_MCConly: 567
+ValveHoldTime_x100us_DAC_MCConly: 781
+HKTRIGGERtoFlashlampDelayTime_x434ns_DAC_MCConly: 205
+FlashlampPulseLength_x434ns_DAC_MCConly: 34
+CameraPulseLength_x434ns_DAC_MCConly: 505
+SyringeSampleVolume: 5.000000
+blobYgrowAmount: 5
+minimumGapBewtweenAdjacentBlobs: 50
+focusMotorSmallStep_ms: 25
+focusMotorLargeStep_ms: 200
+PMTAtriggerThreshold_DAQ_MCConly: 0.150000
+PMTBtriggerThreshold_DAQ_MCConly: 0.150000
+PMTCtriggerThreshold_DAQ_MCConly: 0.000000
+PMTDtriggerThreshold_DAQ_MCConly: 0.000000
+PMTtriggerSelection_DAQ_MCConly: 3
+ADCPGA_DAQ_MCConly: 1
+triggerAckTimeout_x34720ns_DAQ_MCConly: 21600
+pulseStretchTime_x2170ns_DAQ_MCConly: 18
+debubbleWithSample: 0
+pumpDriveVoltage: 24.000000
+autoWindowsShutdown: 0
+NumberSyringesToAutoRun: 3
+intervalBetweenAlternateHardwareSettings: 0
+altPMTATriggerThreshold_DAQ_MCConly: 0.000000
+altPMTBTriggerThreshold_DAQ_MCConly: 0.000000
+altPMTCTriggerThreshold_DAQ_MCConly: 0.000000
+altPMTDTriggerThreshold_DAQ_MCConly: 0.000000
+altPMTAHighVoltage: 0.000000
+altPMTBHighVoltage: 0.000000
+altPMTCHighVoltage: 0.000000
+altADCPGA_DAQ_MCConly: 0
+altPMTtriggerSelection_DAQ_MCConly: 0
+NumberSyringesBetweenBeadsRun: 0
+laserMotorSmallStep_ms: 500
+laserMotorLargeStep_ms: 50000
+altSyringeSampleVolume: 0.100000
+maximumPulseLength_x2170ns_DAQ_MCConly: 13823
+expertTabVisible: 1
+TCPport: 12345
+HumidityAlarmThreshold(%): 80.000000
+PumpStates: 2
+BeadsSampleVolume: 2.500000
+RunFastFactor: 10.000000
+TimeoutForFirstFrame: 90000
+sampleVolume2skip: 0.000000
+altSampleVolume2skip: 0.000000
+altSamplePortNumber: 8
+primeSampleTube: 0
+stainSample_manual: 0
+StainAuto_auto: 0
+Alt_FlashlampControlVoltage: 0.000000
+stainTime: 30
+rinseOption: 0
+primaryIntakePort: 8
+secondaryIntakePort: 8
+normSamplePortNumber: 8
+replaceFromSecondary: 0
+syringeSamplingSpeed: 716963
+baseSyringeSamplingSpeed: 8962
+runSampleFast: 1
+laserState: 65537
+fill2bypassFilterState: 0
+fill3newSheathState: 0
+LockFilterSlider: 0
+syringeSize: 5
+hasCamera: 1
+AcousticFocusingOnALT: 0
+RefillAfterDebubble: 0
+FileComment: UNDERWAY
+PZTvolts: 40
+PZTfrequency: 1772000
+TemperatureAdjust: 0
+TemperatureAdjust: 0
+FreqUpdateInterval: 3
+DoFreqScan: 0
+StartFreq: 1772000.000000
+FreqStep: 500.000000
+EndFreq: 1800000.000000
+StepDuration: 15000.000000
+stepCount: 1
+Tadjm: 2493.000000
+Tadjb: 1690500.000000
+Tadjm2: 0.000000
+beadSampleTotalVolume: 2.400000
+backflushAfterSampleNoRefill: 0
+HasFastTriggerMod: 0
+BleachToExhaust: 0
+PrimeIntakeVolume: 5.000000
+PromptForFileComment: 0
+DebubbleNeedleVolume: 1.000000
+DebubbleConeVolume: 2.000000
+DebubbleRefillVolume: 3.500000
+DebubbleRefillVolumeInjected: 3.000000
+BypassFieldLimits: 0
+BleachRinseCount: 5
+HasCommandsWindow: 1
+EquipmentType: 1
+runType: NORMAL
+runTime: 11.791851
+inhibitTime: 8.869473
+temperature: 27.160471
+humidity: 50.356638
+ADCFileFormat: trigger#, ADC_time, PMTA, PMTB, PMTC, PMTD, peakA, peakB, peakC, peakD, time of flight, grabtimestart, grabtimeend, ROIx, ROIy, ROIwidth, ROIheight, start_byte, comparator_out, STartPoint, SignalLength, status, runTime, inhibitTime

ifcb/tests/test_files/D20230521T210245_IFCB174.hdr

@@ -0,0 +1,132 @@
+SoftwareVersion: 2.5.0.0
+AnalogFirmware: 45
+HousekeepingFirmware: 32
+sampleNumber: 1
+sampleType: Normal
+triggerCount: 1815
+roiCount: 468
+humidity: 53.133032730601975
+temperature: 19.516250095368896
+runTime: 1200.8731944444444
+inhibitTime: 151.66454861111112
+ADCFileFormat: trigger#, ADCtime, PMTA, PMTB, PMTC, PMTD, PeakA, PeakB, PeakC, PeakD, TimeOfFlight, GrabTimeStart, GrabTimeEnd, RoiX, RoiY, RoiWidth, RoiHeight, StartByte, ComparatorOut, StartPoint, SignalLength, Status, RunTime, InhibitTime
+DAQ_MCCserialPort_DAC_MCConly: /dev/ttyS2
+UvModulePresent: False
+UvWithSample: False
+auxPower1: False
+autoStart: False
+InteractiveAutoStart: False
+autoShutdown: False
+HumidityAlarmThreshold(%): 90
+ValveHumidityHysteresis_DAC_MCConly: 567
+FanTemperatureThreshold_DAC_MCConly: 30744
+FanTemperatureHysteresis_DAC_MCConly: 123
+valveDelay: 781
+FlashlampControlVoltage: 2.7999
+HKTRIGGERtoFlashlampDelayTime_x434ns_DAC_MCConly: 120
+FlashlampPulseLength_x434ns_DAC_MCConly: 20
+CameraPulseLength_x434ns_DAC_MCConly: 500
+cameraGain: 6
+binarizeThreshold: 6
+minimumBlobArea: 2000
+blobXgrowAmount: 20
+blobYgrowAmount: 10
+minimumGapBewtweenAdjacentBlobs: 50
+laserState: True
+runningCamera: True
+pump1State: False
+pump2State: True
+stirrer: False
+viewImages: True
+viewRoisOnly: True
+sendTriggerContent: False
+triggerContinuous: False
+continuousTriggerRate: 1
+fill3newSheathState: False
+PMTAtriggerThreshold_DAQ_MCConly: 0.15
+PMTBtriggerThreshold_DAQ_MCConly: 0.14
+PMTCtriggerThreshold_DAQ_MCConly: 0
+PMTDtriggerThreshold_DAQ_MCConly: 0
+ADCdataRateDAQ_MCConly: 240
+integratorSettleTime: 8
+PMTtriggerSelection_DAQ_MCConly: 3
+altPMTtriggerSelection_DAQ_MCConly: 3
+ADCPGA_DAQ_MCConly: 1
+triggerAckTimeout_x34720ns_DAQ_MCConly: 21600
+TimeoutForFirstFrame: 30
+pulseStretchTime_x2170ns_DAQ_MCConly: 21
+maximumPulseLength_x2170ns_DAQ_MCConly: 13823
+hasCamera: True
+liveEnvironment: False
+flash: True
+PMTAhighVoltage: 0.65
+PMTBhighVoltage: 0.55
+intervalBetweenAlternateHardwareSettings: 0
+Alt_FlashlampControlVoltage: 3
+pumpDriveVoltage: 14
+altPMTAHighVoltage: 0.55
+altPMTBHighVoltage: 0.65
+altPMTATriggerThreshold_DAQ_MCConly: 0.13
+altPMTBTriggerThreshold_DAQ_MCConly: 0.13
+viewTriggers: True
+viewGraphs: False
+viewActivity: True
+viewFPS: True
+KloehnPort: /dev/ttyUSB0
+syringeSamplingSpeed: 20
+syringeOffset: 4176
+NumberSyringesToAutoRun: 3
+SyringeSampleVolume: 5
+altSyringeSampleVolume: 5
+sampleVolume2skip: 0
+syringeSize: 5
+primeVolume: 5
+flushVolume: 1
+BleachVolume: 1
+BiocideVolume: 1
+stepsToFullSyringe: 318354
+debubbleWithSample: True
+RefillAfterDebubble: True
+primeSampleTube: False
+backflushWithSample: False
+runBeads: False
+runSampleFast: False
+BeadsSampleVolume: 0.4
+NumberSyringesBetweenBeadsRun: 0
+NumberSyringesBetweenCleaningRun: 0
+RunFastFactor: 5
+viewSyringe: True
+viewValve: True
+focusMotorSmallStep_ms: 50
+focusMotorLargeStep_ms: 500
+laserMotorSmallStep_ms: 500
+laserMotorLargeStep_ms: 5000
+debubbleConeVolume: 2
+debubbleNeedleVolume: 3
+debubbleRefillVolume: 3.5
+debubbleLeftVolume: 0.5
+BleachRinseCount: 3
+BleachRinseVolume: 1
+BleachToExhaust: False
+SamplingFastSpeed: 4
+CounterCleaning: 112
+CounterBeads: 112
+CounterAlt: 112
+imagerID: 174
+DataFilePath: /home/ifcb/ifcbdata/shimada_may2023
+FolderHierarchy: False
+OutputFiles: True
+FileComment: fsw
+triggerThreadCount: 3
+featureThreadCount: 3
+FeaturesVersion: V4
+featureGeneration: False
+SaveBlobs: False
+WebBrowser: chromium
+WebBrowserArguments: --disable-gpu
+GPSFeed: 0
+PhytoArmDataSource: 0
+ServerAsAdmin: False
+HostAsAdmin: False
+UpdateServer: http://mclanelabs.dyndns.org:8082/external/update/ifcbacquire/release/
+TestMode: False