File types

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File type and extensions constants

These constants are file types and extensions. It can be used for filenames testing or with acquisition functions.

Python example: 

# measure and save one 0.25 second frame to png file named "testFile.png"
dev.doSimpleAcquisition(1, 0.25, pixet.PX_FTYPE_PNG, "testFile")
dev.doSimpleAcquisition(1, 0.25, pixet.PX_FTYPE_AUTODETECT, "testFile.png")
File types and extensions constants table
File type constants File extensions constants Exts
PX_FTYPE_NONE (No direct file saving – data stored only in memory)
PX_FTYPE_AUTODETECT (FTYPE detected by extension in a filename)
PX_FTYPE_ASCII_FRAME PX_EXT_ASCII_FRAME "txt"
PX_FTYPE_BINARY_FRAME PX_EXT_BINARY_FRAME "pbf"
PX_FTYPE_MULTI_FRAME PX_EXT_MULTI_FRAME "pmf"
PX_FTYPE_BINARY_MULTIFRAME PX_EXT_BINARY_MULTI_FRAME "bmf"
PX_FTYPE_TPX3_PIXELS PX_EXT_TPX3_PIXELS "t3p"
PX_FTYPE_TPX3_PIXELS_ASCII PX_EXT_TPX3_PIXELS_ASCII "t3pa"
PX_FTYPE_CLUSTER_LOG PX_EXT_CLUSTER_LOG "clog"
PX_FTYPE_PIXEL_LOG PX_EXT_PIXEL_LOG "plog"
PX_FTYPE_PNG PX_EXT_PNG "png"
PX_FTYPE_TPX3_RAW_DATA PX_EXT_TPX3_RAW_DATA "t3r"
PX_FTYPE_PIXET_RAW_DATA PX_EXT_PIXET_RAW_DATA "prd"
PX_FTYPE_EXTERNAL (reserved)
(description file saved automatically with pmf/txt) PX_EXT_FRAME_DESC "dsc"
(index file saved automatically with pmf/txt) PX_EXT_INDEX "idx"
Files extensions summary
txt ASCII matrix: Text files with img lines converted to text lines with numbers separated by spaces.
pbf Simple binary files, numbers only.
pmf Multiple frames. Default is same as the txt, but multiple frames on top of each other. Can use BINARY flag.
t3pa Tpx3 pixels ASCII. Text format, tab-separated columns with the header in the first row. Biggest to saving.
t3p Tpx3 pixels. Binary format. Lower saved size, more complex to understand.
t3r Tpx3 raw data. Fastest to saving, difficult to understand, slow to processing and can cause processing errors.
bstg Binary settings file: Measured data with all configuration. See Binary Spectral Imaging API: BSTG files
clog, plog Clusters/pixels logs. Text files contains clusters separated to frames with pixels lists. Historic formats for saving a data with few hited pixels in a frames.
h5 HDF5, hierarchical data format 5. Used as one of multi-frame formats.
info Text file with "[FileInfo]" head and all metadata list.
dsc Text file with frame index first and all metadata list.
idx Binary index for multi-frame files. Usesfull for fast access to n-th frame.

File saving flags summary

File saving flags can do additional settings for file(s) saving.

  • Can be used in saving files or in doAdvancedAcquisition python methods, for example.
  • Flags can be combined.
  • Default frame file settings is set of separate subframes text files, with all pixels include zeros, each subframe with idx+dsc files:
file_ToT.pmf, file_ToT.pmf.dsc, file_ToT.pmf.idx, file_ToA.pmf, file_ToA.pmf.dsc, file_ToA.pmf.idx
File saving flags
Flag constant base name Description
PX_FRAMESAVE_BINARY Use binary format in pmf.
PX_FRAMESAVE_SPARSEX Index + non-zero pixels in file. # separates (sub)frs.
PX_FRAMESAVE_SPARSEXY X, Y + non-zero pixel in file. # separates (sub)frames.
PX_FRAMESAVE_NODSC Do not add dsc file.
PX_FRAMESAVE_NOSUBFRAMES Do not use subframes, save main frame only.
PX_FRAMESAVE_SUBFRAMES_ONEFILE Save all subframes to a single file.
PX_FRAMESAVE_SUBFRAMES_SAVEMAINFRAME Save separate all subframes and main frame extra.


The file saving flags can be used in
  • Python API: Use pixet.PX_FRAMESAVE_... constants in flags parameter of some measuring/saving methods.
  • Binary API: Use PX_FRAMESAVE_... constants in flags parameter of some measuring functions.
  • The Pixet program. Available in the More measurement settings, after filename was selected
File saving flags in More measurement settings in Pixet
File saving flags in More measurement settings in Pixet

File extensions and flags: TXT/PBF/PMF/BMF details

The files formats

txt Single frame in the text file.
pbf Pixet Binary Frame - Single frame in the binary file.
pmf Pixet Multi Frame - Multiframe file with text or binary format, depends on flags used with saving.
bmf Binary Multi Frame - Multiframe file with binary format, depends on flags used with saving.
idx Index for seeking - Binary array of 64b pointers to start of frames and subframes.
dsc Description. List of all metadata for each frame and subframe. Actual device and acquisition parameters, data types, etc. The "Frame name" item can be helpful to orientation in pmf structure if the ONEFILE flag used. The Type=item is helpful to understanding the structure of data if the BINARY flag used.

Multi-files names generation

Note
All the next examples are for Timepix3, single chip, opm = TPX3_OPM_TOATOT


flags 0 (default), input filename = "name", acqCount = 1
name_ToA.txt, name_ToA.txt.dsc, name_ToT.txt, name_ToT.txt.dsc


acqCount = 6
name_0_ToA.txt, name_0_ToA.txt.dsc, name_0_ToT.txt, ...
...
name_5_ToA.txt, name_5_ToA.txt.dsc, ...


PMF note
With each pmf generating .pmf.idx binary file, other is same as TXT with acqCount = 1.

Files with flags=0

Note
All the next examples are for Timepix3, single chip, opm = TPX3_OPM_TOATOT


TXT file data, default
0 0 0 5 0 0 0 … 256 numbers (int for non-calibrated values or float if the calibration used) and enter
0 872 0 0 0 … 256 numbers (int for non-calibrated values or float if the calibration used) and enter
(256 lines)


PMF file data, default
0.00000 78.65742 0.00000 … 256 numbers (int for non-calibrated values or float if the calibration used) and enter
0.00000 0.00000 999785.5 … 256 numbers (int for non-calibrated values or float if the calibration used) and enter
(256 lines * acqCount)

Flags influence to files

TXT file data: FRAMESAVE_SPARSEX flag
_ToA.txt file _ToT.txt file
px index ToA px index ToT
0 227212.500000 0 20
17 310685.937500 17 13
255 265487.500000 255 11
1274 105728.125000 1274 9
- Lists of all hited pixels
- ToT: int for non-calibrated data or float if the calibration used


TXT file data: FRAMESAVE_SPARSEXY flag
_ToA.txt file _ToT.txt file
X Y ToA X Y ToT
247 3 189851.562500 247 3 16
250 4 140042.187500 250 4 12
5 9 317195.312500 5 9 5
- Lists of all hited pixels
- ToT: int for non-calibrated data or float if the calibration used


PMF file data, pixet.PX_FRAMESAVE_SPARSEX(Y) flag
Same as TXT, but containing single lines with only # to separate frames

X Y ToA Line description
232 139 321620.312500 frame 1, px 1
4 252 340231.250000 frame 1, px 2
# frames separator
39 0 258270.312500 frame 2, px 1
201 0 76593.750000 frame 2, px 2
92 1 268642.187500 frame 2, px 3


PX_FRAMESAVE_SUBFRAMES_ONEFILE
All the data is in one file, subframes are placed one behind the other. If the measurement result has 10 frames with 2 subframes A/B, each _n TXT file contains 2 subrfames and the PMF contains 20 frames in order:
sfr0A, sfr0B, sfr1A, sfr1B, ...
The exact order and names of type of (sub)frames is listed in the DSC file. The DSC have separate records [Fn] for all the items.


PX_FRAMESAVE_SUBFRAMES_SAVEMAINFRAME
The group of the saved files contains the main frame and all subframes. Subframe files end in _sfrName, the main frame does not. In DSC file accompanying the TXT with main frame is not the "Frame name" item.
Not applicable if combined with the ONEFILE flag.


PX_FRAMESAVE_BINARY
If the file type supports text and binary format, ex. PMF, save the binary.
Not applicable to TXT, must use PBF instead.
Data in the file are the simple array of non-calibrated 16 or 32b integers or calibrated doubles. See the DSC file for used data type.


BINARY + SPARSEXY examples:   
Example of data saved if flags BINARY+SPARSEXY used
Example of data saved if flags BINARY+SPARSEXY used

DSC files details

The first 3 lines have special functions:

  1. File type selection
  2. Index of the frame in this file
  3. Arrangement and type of the data

Other lines are a list of metadata items separated by blank lines.
In txt.dsc and pbf.dsc, end of the frame is end of the file.
In the pmf.dsc, next item 2 and 3 and frame or subframe data follows.


Some example (PBF 1 frame, with BINARY and SPARSEXY – test_49_ToA.pbf.dsc): 

B000000001                                      B=binary / A=ASCII and number = count of frames in multiframe file
[F0]                                            Index of frame in the file = 0
Type=double [X,Y,C] width=256 height=256        Data type double, X,Y,C = only hit pixels saved and has XY pos.
"Acq Serie Index" ("Acquisition serie index"):  Some metadata item name and (description)
u32[1]                                          Type of the item data [number of values]
49                                              The value

(more metadata items separated by blank lines …)

"Frame name" ("Frame name"):
char[3]
ToA                                             This is the ToA frame

(more metadata items separated by blank lines …)
(end of the file)
Data format options
matrix - Whole matrix saved. Number of saved pixels are allways width*height
[X,C] - Hit pixels only. Every saved pixel has matrix index and data value.
[X,Y,C] - Hit pixels only. Every saved pixel has X,Y position and data value.


Other example (PMF 10 frames, with BINARY+SPARSEX+ONEFILE – test.pmf.dsc): 

B000000010
[F0]                                            Start of the first subframe
Type=double [X,C] width=256 height=256          Pixel index and double type pixel data (ToA in ns)
"Acq Serie Index" ("Acquisition serie index"):
u32[1]
0 

(more metadata items separated by blank lines …)

"Frame name" ("Frame name"):
char[3]
ToA 
(more metadata items separated by blank lines …)

[F1]                                            Start of the second subframe
Type=i16 [X,C] width=256 height=256             Pixel index and i16 type pixel data (ToT in ticks 40MHz)
"Acq Serie Index" ("Acquisition serie index"):
u32[1]
0

(and the ToT frame metadata, [F2] and ToA subframe, [F3] and ToT sfr, … [Fn] and ToT sfr of (n/2)th frame)


Complete one frame DSC example (PMF 1 frame, BINARY+SPARSEX – test_15_ToA.pbf.dsc): 

B000000001
[F0]
Type=double [X,C] width=256 height=256
"Acq Serie Index" ("Acquisition serie index"):
u32[1]
15

"Acq Serie Start time" ("Acquisition serie start time"):
double[1]
1639059034.903085 
"Acq time" ("Acquisition time [s]"):
double[1]
0.500000

"ChipboardID" ("Chipboard ID"):
char[9]
I08-W0060

"DACs" ("DACs"):
u16[19]
16 8 128 10 120 1301 501 5 16 8 16 8 40 128 128 128 256 128 128 

"Frame name" ("Frame name"):
char[3]
ToA

"HV" ("High voltage [V]"):
double[1]
-500 

"Interface" ("Readout interface"):
char[7]
MiniPIX

"Mpx type" ("Medipix type (1-MXR, 2-TPX, 3-MPX3, 4-TPX3, 5-TPX2)"):
i32[1]
4 

"Pixet version" ("Pixet version"):
char[5]
1.7.8

"Start time" ("Acquisition start time"):
double[1]
1639059042.934810 

"Start time (string)" ("Acquisition start time (string)"):
char[64]
Thu Dec 9 15:10:42.934809 2021

"Threshold" ("Threshold [keV]"):
double[1]
5.026744

IDX files details

The IDX files are generated with multiframe files to help with fast seeking frames in files. Each frame except first has the basic structure in the IDX file: 

struct IndexItem {
 i64 dscPos;    // frame position in the DSC file
 i64 dataPos;   // frame position in the main data file
 i64 sfPos;     // subframe position if exist subframes file next to the main data file (usually not and =0)
};

The PMF.IDX files generated beside the PMFs. Contains the simple binary array of structs of 3 little-endian qwords with addresses associated to the start of each frame except first: DSC, frame and subframe.

.pmf.idx with BINARY+ONEFILE, ToA+ToT example
main data contains
  • ToA subframes (double*0x10000 = len 0x80000)
  • ToT subframes (i16*0x10000 = len 0x20000)

The IDX contains

  1. Pointers to frames in DSC file at 0 (not in idx), 0x03B5, 0x075D, 0x0B08, 0x0BE0, ...
  2. Pointers to frames in main data file at 0 (not in idx), 0x080000, 0x0A0000, 0x120000, 0x140000, 0x1C0000, ...
  3. Pointers to frames in additional subframes file (not exist -> all=0)
.pmf.idx file example
.pmf.idx file example

T3PA files details

The T3PA is timepix3 data file in text format with lines and tabs. Contains the information line and data lines with record index, pixel index in the matrix, Time of arrival, Time over threshold, Fine ToA and Overflow.
Example: 

Index   Matrix Index    ToA     ToT     FToA    Overflow
0       1028    1918    14      22      0
1       1028    3126    8       28      0
2       1028    3778    5       23      0
...
156003  39793   98473646054     38      9       0
156004  190     98492090610     19      3       0
  • The Index is simple index of measurement line. This growing while measurement is running. If you append new measurement to existing file, new index is 0 again and again growing while new measurement is running.
Physical position of the x=0, y=0 pixel on the Minipix (1,1 in Pixet view)
Physical position of the x=0, y=0 pixel on the Minipix (1,1 in Pixet view)
  • The Matrix Index is index of the pixel. On the Minipix Tpx3 is 0 at the left-down (see image)
  • The ToA is time of arrival in units 25 ns, mod by limit, for example Minipix 264 (14600y), Advapix-single 230 (26s), Advapix-Quad 228 (6.5s).
Note: The ToA on-chip implementation in the pixels is limited to 14 bits (409.6 µs).
The ToA in T3PA is extended by device. But there is inherent uncertainty around the borders. These values may be incorrectly assigned. Users not comfortable with our extension can apply AND with (uint64)16383 to extended ToA to get original ToA from the chip.
  • The ToT is time over threshold in units 25 ns.
  • The FToA stands for "fine ToA" and it is the finest step of the ToA measurement. To properly account for this step in the conversion of ToA to time, it is necessary to subtract the amount of counts of fToA in the following manner:
Time [ns] = 25*ToA - (25/16)*fToA
The original range of this fToA value in the chip is 4 bits, or 16 values. This is extended in the post-processing of the data into 5 bits, or 32 values to include a correction for the delay of the clock propagation in the chip. The final value exported into t3pa files has a range of 5 bits, or 32 values, but the previous equation still stands.
  • The Overflow is sign of data transfer overflow. If the line has this 1:
index = 0x74: start of lost data
index = 0x75: end of lost data, toa is length of the missing time
(this can occurs with rates over megahits per seconds for Minipix)
Note: In data from multichip devices, there is not Overflow, replaced by Chip index (But column name is still Overflow).


If saving of the T3PA repeated to the same file, new data will be append with new reset of record index and ToA and the file containing parts is like this: 

507812	353	39993345	1022	15	0
507813	46177	39999843	159	2	0
507814	45921	39999843	159	2	0
0	421	2	13	29	0
1	297	2	22	27	0
2	297	145	62	17	0
3	297	283	19	13	0

CLOG and CLOG.IDX files details

The CLOG format was developed to facilitate further processing of cluster data by the user programs. This is a text file divided to the frame records and the records can contain a clusters. Frames and clusters are separated by the line breaks. Frames can be separated by whole free line.

The record format
Frame FN (frameStart, frameAcqTime s)
[x, y, energy, ToA] [x, y, energy, ToA] [x, y, energy, ToA] …


FN Frame index number. First 0 or 1.
frameStart Start time of the frame. There are variants:

1. If it from measuring or from replay frame-based data with metadata available:

Linux format, frame starting time from PC’s getPrecisionTime.

2. If it from pixel-based data with metadata available (file.t3pa + file.t3pa.info):

Linux format, acq. starting time from PC’s getPrecisionTime with added time from data.

3. If it from replay data and metadata not available:

Nanoseconds from the input data.
Periodic increments if source is frame-based, random increments if source is data-driven.
frameAcqTime    Duration of the frame, float in seconds. Always 0.000000 in data from data-driven sources.
x, y Position of the pixel.
energy* Energy deposited in the pixel. Integer ToT counter value if not calibrated, float in keV if calibrated.
ToA* Time of arrival, relative to frameStart. Integer in CLK ticks if ToA conversion is disabled, float in ns if ToA conversion is enabled.

*ToA+energy records can be created from source that supports combined ToA+ToT modes, like as OPM_TOATOT on the Timepix3. If the data source supports only single modes, only one value is in this position.

Clog from data-driven source not contains free frames.
Clog from frame-based source can contains free frames.


Example records (Timepix3, Frame2 with two clusters by 2 and 4 pixels, Frame3 with single 2-pixel cluster) 

Frame 2 (273697060.937500, 0.000000 s)
[214, 195, 43.1598, 0] [220, 191, 20.6515, 7.8125]
[224, 182, 21.8018, 31.25] [223, 186, 4.58576, 31.25] [222, 183, 38.2381, 31.25] [226, 185, 14.7623, 34.375]

Frame 3 (371034565.625000, 0.000000 s)
[151, 33, 32.5745, 0] [151, 34, 13.8135, 17.1875]


Example records (Timepix) 

Frame 6 (1639143482.765164, 0.200000 s)
[87, 134, 5.75352] [217, 58, 14.8396]
Frame 7 (1639143483.019154, 0.200000 s)
Frame 8 (1639143483.261158, 0.200000 s)
Frame 9 (1639143483.513150, 0.200000 s)


The CLOG.IDX files generated beside the CLOGs. Contains the simple binary array of little-endian qword addresses of the "F" at each record start.
.clog.idx example
Pointers to records at 0, 0x29, 0x52, 0x7b, 0xA4, 0xCD, ...
Example .clog.idx file
Example .clog.idx file

Pixel matrix configuration files

Overview
bpc    Binary Pixel Configuration All PM config in one file, meaning of the bits depends on the chip.
txt Ascii Mask Matrix Text file with pixel mask
txt Ascii Test Bit Matrix Text file with test bits
txt Ascii THL adj. bits Matrix Text file with threshold values adjustment

Other files

  • H5: The HDF5 files. Binary containers for structured data. If used to save, contains both measured data and metadata.
To access theese files, use third party tools like as HDFview from HDF Group, libraries like as h5py for Python or HDF5 C++ API from HDF Group.

Related

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