snAPI v 1.1.2.1

- add custom tags (in snAPI)
- fix Unfold in UniHarp for less counts
- add Demo_Imaging_PTU.py

Author: tpoint75

demos/Demo_Imaging_PTU.py

@@ -0,0 +1,115 @@
+from snAPI.Main import *
+import matplotlib
+
+matplotlib.use("TkAgg", force=True)
+from matplotlib import pyplot as plt
+
+if __name__ == "__main__":
+
+    sn = snAPI()
+    sn.getDevice("1000509")
+    sn.initDevice(MeasMode.T2)
+
+    sn.loadIniConfig(r"config\HH500.ini")
+
+    history_size = 1
+    sn.setLogLevel(LogLevel.DataFile, True)
+    sn.timeTrace.setNumBins(10000)
+    sn.timeTrace.setHistorySize(history_size)
+    
+    
+    # set Marker (1..4)
+    sn.device.setMarkerEdges(1, 0, 0, 0)
+    sn.device.setMarkerEnable(1, 1, 1, 0)
+    
+    # set Image Tag
+    sn.setMeasurementSubMode(subMode=MeasSubMode.Image)
+    # Marker (1) in TTTR stream defining a line start
+    sn.addIntTag("ImgHdr_LineStart", 1)
+    # Marker (2) in TTTR stream defining a line start
+    sn.addIntTag("ImgHdr_LineStop", 2)
+    # Marker (3) in TTTR stream defining a frame change
+    sn.addIntTag("ImgHdr_Frame", 3)
+        
+    #  Dimension of the measurement: 1 = Point; 2 = Line; 3 = Image; 4 = Stack
+    sn.addIntTag("ImgHdr_Dimensions", 3)
+    
+    # Identifies the scanner hardware: 
+    # (1 = PI E-710; 3 = LSM; 5 = PI Line WBS; 6 = PI E-725; 7 = PI E-727; 8 = MCL; 9 = FLIMBee; 10 = ScanBox)
+    #sn.addIntTag("ImgHdr_Ident", 3)
+    
+    # Scan direction, defining the configuration of fast and slowscan axis
+    # First Axis = Fast Scan axis, Second Axis = SlowAxis
+    # PI_SCANMODE_XY(0) = X-Y Scan (default)
+    # PI_SCANMODE_XZ(1) = X-Z Scan
+    # PI_SCANMODE_YZ(2) = Y-Z Scan
+    #sn.addIntTag("ImgHdr_ScanDirection", 0)
+    
+    # Scan pattern:
+    # TRUE identifies bidirectional scanning
+    #  1st line forward scan
+    #  2nd line backward scan
+    #  3rd line forward 
+    #  4th line backward; ...)
+    # FALSE identifies monodirectional scanning (all lines forward - default)
+    #sn.addBoolTag("ImgHdr_BiDirect", False)
+
+    # If > 0, the image was recorded using a sinuidal instead of a linear movement
+    # Value represents percentage of the sinus wave used for the measurement (0-100%)
+    # (default: 0)
+    #sn.addIntTag("ImgHdr_SinCorrection", 0)
+
+    # [ms]
+    # Integration time per pixel for image measurements
+    sn.addIntTag("ImgHdr_TimePerPixel", 20)
+    
+    # [µm]
+    # X, Y, Z Position of measurement (interpretation depends on ImgHdr_Dimensions 
+    # for point measurements: the coordinate of measurement 
+    # for line: the start point 
+    # for images: the offset of the upper left edge of the image)
+    sn.addFloatTag("ImgHdr_X0", 0.0)
+    sn.addFloatTag("ImgHdr_Y0", 0.0)
+    sn.addFloatTag("ImgHdr_Z0", 0.0)
+    
+    # Number of pixels in the fast scan direction (for image measurements)
+    sn.addIntTag("ImgHdr_PixX", 256)
+    # Number of pixels in the slow scan direction (for image measurements)
+    sn.addIntTag("ImgHdr_PixY", 256)
+    #  [µm]; Resolution of a single pixel (line and image measurements)
+    sn.addFloatTag("ImgHdr_PixResol", 1.0)
+    
+    #sn.addIntTag("TestInt", 9223372036854775807, 123)
+    #sn.addFloatArrayTag("TestFloatArray", [1.1, 2.3, 3.3, 4.4])
+    #sn.addByteArrayTag("TestIntArray", [0,1,2,3,4,0,0,0])
+        
+    # set the file name
+    sn.setPTUFilePath("out.ptu")
+
+    sn.timeTrace.measure(int(history_size * 1e3), waitFinished=False, savePTU=True)
+    ft = 0
+    while True:
+        finished = sn.timeTrace.isFinished()
+        #if finished:
+        #    sn.timeTrace.t0.value = 0
+        counts, times = sn.timeTrace.getData()
+        plt.clf()
+
+        plt.plot(times, counts[0], linewidth=2.0, label="sync")
+        for c in range(1, 1 + sn.deviceConfig["NumChans"]):
+            plt.plot(times, counts[c], linewidth=2.0, label=f"chan{c}")
+        plt.grid()
+        plt.xlabel("Time [s]")
+        plt.ylabel("Counts[Cts/s]")
+        plt.yscale('log', base=10, nonpositive='clip')
+        plt.legend()
+        plt.title("TimeTrace")
+        plt.pause(0.1)
+
+        if finished:
+            ft+=1
+            if ft > 10:
+                break
+
+    plt.show(block=True)
+    plt.close()

demos/config/HH500.ini

@@ -0,0 +1,17 @@
+[Device]
+HystCode = 0
+SyncDiv = 1
+SyncEdgeTrig = -50,1
+SyncChannelOffset = 0
+SyncChannelEnable = 1
+SyncDeadTime = 0
+StopCount = 0
+Binning = 1
+Offset = 0
+TriggerOutput = 0
+
+[All_Channels]
+EdgeTrig = -50,1
+ChanOffs = 0
+ChanEna = 1
+DeadTime = 0

dist/snapi-1.1.0.tar.gz

@@ -0,0 +1,5 @@
+PQ Tag Dictionary
+-----------------
+
+.. raw:: html
+    :file: _static/tables/PQTagDictionary.html

…se/snapi-1.1.0-cp311-cp311-win_amd64.whl …st/snapi-1.1.2-cp313-cp313-win_amd64.whlwheelhouse/snapi-1.1.0-cp311-cp311-win_amd64.whl renamed to dist/snapi-1.1.2-cp313-cp313-win_amd64.whl wheelhouse/snapi-1.1.0-cp311-cp311-win_amd64.whl renamed to dist/snapi-1.1.2-cp313-cp313-win_amd64.whl

@@ -0,0 +1,33 @@
+PQ Tag Types
+------------
+
+.. note::
+    
+    - Tag region of files have always lengths divisible by 8
+    - In files, tags start always on positions divisible by 8.
+    - Tag_Id is case sensitive.
+
+File Magic
+""""""""""
+
+The following table gives the file type identifying "magics" as to be found in preamble 1. 
+This preamble is filled up to its full length of 8 with '\0'.
+
+.. raw:: html
+    :file: _static/tables/PQTagFileMagics.html
+
+Tag Format Definition
+"""""""""""""""""""""
+
+The following table illustrates the format of valid tags. It is described as a structure with named fields:
+
+.. raw:: html
+    :file: _static/tables/PQTagFormatDefinition.html
+
+Tag Type Definition
+"""""""""""""""""""
+
+The following table defines the types of valid tags with their domain and additional length if enhanced:
+
+.. raw:: html
+    :file: _static/tables/PQTagTypes.html

dist/snapi-1.1.2.tar.gz

@@ -15,8 +15,10 @@ Welcome to snAPI's documentation!
    install
    snAPI
    config
-   tttr data format
    hardware
+   tttr data format
+   PQTag_Dictionary
+   PQTag_Types
 
 Indices and tables
 ==================

doc_source/PQTag_Dictionary.rst

@@ -1,15 +1,22 @@
 TTTR Record Format
 ==================
 
+This describes the structure of the PTU-Files with its header, tags and time tag data. 
+
+Important Documents
+-------------------
+
+- `Tag Dictionary <PQTag_Dictionary.html#pq-tag-dictionary>`_
+- `Tag Types <PQTag_Types.html#tag-type-definition>`_
+- `Tag Format <PQTag_Types.html#tag-format-definition>`_
+- `File Magic <PQTag_Types.html#file-magic>`_
+
 Basic record format
----------------------
+-------------------
 
 This page describes the format of the TTTR data named as raw data in ptu files.
-
 Due to performance reasons the TTTR data are saved exactly as received from TCSPC device, hence the format of the TTTR records depends on the kind of TCSPC device and the type of measurement. The record format used in a particular file is denoted in the mandatory tag TTResultFormat_TTTRRecType.
-
 Even though the record formats differ, the formal algorithms for the calculations on them don't: To get the global arrival time of a photon or a marker in seconds, count the overflows until the current position and multiply with the overflow period, then add the timetag (for T2) or nSync (for T3) and multiply with the MeasDesc_GlobalResolution.
-
 The arrival time since the last sync event in T3 measurements is denoted in dTime. To get the time in seconds multiply dTime with MeasDesc_Resolution.
 
 Images
@@ -121,4 +128,4 @@ The channel code 15 (0xF) marks a special record.
 Special records can be overflows or external markers. To differentiate this, dTime must be checked.
 
 If it is zero, the record marks an overflow.
-If it is >=1 the individual bits are external markers.
+If it is >=1 the individual bits are external markers.

doc_source/PQTag_Types.rst

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: f357dabe0031662a7e3ad0888c85f0a0
+tags: 645f666f9bcd5a90fca523b33c5a78b7