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Make a library for writing and reading tiff, added tests (#347)

Browse Source 
* removed Makefile for moench and integrated the build in CMake
* broke out tiff reading and writing to its own library
* moved tiff includes to include/sls
* moved tiffio source to src
* removed incorrectly used bps
* cleanup and tests for tiffio
* removed using namespace std from header
* some fixing for moench04
* Program for offline processing renamed

Co-authored-by: Anna Bergamaschi <anna.bergamaschi@psi.ch>
This commit is contained in:
Erik Fröjdh
2022-01-27 10:24:02 +01:00
committed by GitHub
parent 379d08dd03
commit f6e76145c1
32 changed files with 4948 additions and 2143 deletions
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22
slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNew.h
View File

@ -107,8 +107,8 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
#endif
if (dataMap[row][col] < 0 ||
dataMap[row][col] >= nSamples * 2 * 32)
cout << "Error: pointer " << dataMap[row][col]
<< " out of range " << endl;
std::cout << "Error: pointer " << dataMap[row][col]
<< " out of range " << std::endl;
}
}
}
@ -120,7 +120,7 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
ghost[iy][ix] = 0.;
int ipacket;
int ibyte;
uint ibyte;
int ii = 0;
for (ibyte = 0; ibyte < sizeof(sls_detector_header) / 2; ibyte++) {
xmap[ibyte] = -1;
@ -298,17 +298,17 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
/* return NULL; */
/* }; */
virtual char *readNextFrame(ifstream &filebin) {
virtual char *readNextFrame(std::ifstream &filebin) {
int ff = -1, np = -1;
return readNextFrame(filebin, ff, np);
};
virtual char *readNextFrame(ifstream &filebin, int &ff) {
virtual char *readNextFrame(std::ifstream &filebin, int &ff) {
int np = -1;
return readNextFrame(filebin, ff, np);
};
virtual char *readNextFrame(ifstream &filebin, int &ff, int &np) {
virtual char *readNextFrame(std::ifstream &filebin, int &ff, int &np) {
char *data = new char[dataSize];
char *d = readNextFrame(filebin, ff, np, data);
if (d == NULL) {
@ -318,17 +318,13 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
return data;
}
virtual char *readNextFrame(ifstream &filebin, int &ff, int &np,
virtual char *readNextFrame(std::ifstream &filebin, int &ff, int &np,
char *data) {
char *retval = 0;
int nd;
int fnum = -1;
np = 0;
int pn;
// cout << dataSize << endl;
if (ff >= 0)
fnum = ff;
if (filebin.is_open()) {
if (filebin.read(data, dataSize)) {

14
slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h
View File

@ -29,7 +29,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
moench03T1ZmqDataNew(int ns = 5000, int oo = 2 * 2)
: slsDetectorData<uint16_t>(400, 400, ns * 32 * 2 + oo), nSamples(ns),
offset(oo), xtalk(0.00021) {
cout << "M0.3" << endl;
std::cout << "M0.3" << std::endl;
int nadc = 32;
int sc_width = 25;
int sc_height = 200;
@ -70,8 +70,8 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
dataMap[row][col] =
(nadc * i + iadc) * 2 + offset; //+16*(ip+1);
if (dataMap[row][col] < 0 || dataMap[row][col] >= dataSize)
cout << "Error: pointer " << dataMap[row][col]
<< " out of range " << endl;
std::cout << "Error: pointer " << dataMap[row][col]
<< " out of range " << std::endl;
}
}
}
@ -260,17 +260,17 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
/* return NULL; */
/* }; */
virtual char *readNextFrame(ifstream &filebin) {
virtual char *readNextFrame(std::ifstream &filebin) {
int ff = -1, np = -1;
return readNextFrame(filebin, ff, np);
};
virtual char *readNextFrame(ifstream &filebin, int &ff) {
virtual char *readNextFrame(std::ifstream &filebin, int &ff) {
int np = -1;
return readNextFrame(filebin, ff, np);
};
virtual char *readNextFrame(ifstream &filebin, int &ff, int &np) {
virtual char *readNextFrame(std::ifstream &filebin, int &ff, int &np) {
char *data = new char[32 * 2 * nSamples];
char *d = readNextFrame(filebin, ff, np, data);
if (d == NULL) {
@ -280,7 +280,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
return data;
}
virtual char *readNextFrame(ifstream &filebin, int &ff, int &np,
virtual char *readNextFrame(std::ifstream &filebin, int &ff, int &np,
char *data) {
// char *retval=0;
// int nd;

247
slsDetectorCalibration/dataStructures/moench04CtbZmq10GbData.h
View File

@ -3,50 +3,9 @@
#ifndef MOENCH04ZMQ10GBDATA_H
#define MOENCH04ZMQ10GBDATA_H
#include "slsDetectorData.h"
#include "sls/sls_detector_defs.h"
#ifndef SLS_DETECTOR_HEADER
#define SLS_DETECTOR_HEADER
//#define VERSION_V2
/**
@short structure for a Detector Packet or Image Header
@li frameNumber is the frame number
@li expLength is the subframe number (32 bit eiger) or real time exposure
time in 100ns (others)
@li packetNumber is the packet number
@li bunchId is the bunch id from beamline
@li timestamp is the time stamp with 10 MHz clock
@li modId is the unique module id (unique even for left, right, top, bottom)
@li xCoord is the x coordinate in the complete detector system
@li yCoord is the y coordinate in the complete detector system
@li zCoord is the z coordinate in the complete detector system
@li debug is for debugging purposes
@li roundRNumber is the round robin set number
@li detType is the detector type see :: detectorType
@li version is the version number of this structure format
*/
typedef struct {
uint64_t frameNumber; /**< is the frame number */
uint32_t expLength; /**< is the subframe number (32 bit eiger) or real time
exposure time in 100ns (others) */
uint32_t packetNumber; /**< is the packet number */
uint64_t bunchId; /**< is the bunch id from beamline */
uint64_t timestamp; /**< is the time stamp with 10 MHz clock */
uint16_t modId; /**< is the unique module id (unique even for left, right,
top, bottom) */
uint16_t xCoord; /**< is the x coordinate in the complete detector system */
uint16_t yCoord; /**< is the y coordinate in the complete detector system */
uint16_t zCoord; /**< is the z coordinate in the complete detector system */
uint32_t debug; /**< is for debugging purposes */
uint16_t roundRNumber; /**< is the round robin set number */
uint8_t detType; /**< is the detector type see :: detectorType */
uint8_t version; /**< is the version number of this structure format */
uint64_t
packetCaught[8]; /**< is the version number of this structure format */
} sls_detector_header;
#endif
using namespace std;
class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
private:
@ -68,67 +27,40 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
// moench04CtbZmq10GbData(int nas=5000, int nds=0):
// slsDetectorData<uint16_t>(400, 400, nas*2*32+nds*8), aSamples(nas),
// dSamples(nds), nadc(32), sc_width(25), sc_height(200) {
#ifndef RAWDATA
moench04CtbZmq10GbData(int nas = 5000, int nds = 0)
: slsDetectorData<uint16_t>(400, 400,
(nas > 0) && (nds > 0)
? max(nas, nds) * (32 * 2 + 8)
: nas * 32 * 2 + nds * 8),
nadc(32), sc_width(25), sc_height(200), aSamples(nas), dSamples(nds) {
int off = 0;
#endif
#ifdef RAWDATA
moench04CtbZmq10GbData(int nas = 5000, int nds = 0)
: slsDetectorData<uint16_t>(400, 400,
sizeof(sls_detector_header) +
#ifdef RAWDATA
sizeof(slsDetectorDefs::sls_receiver_header) +
#endif
((nas > 0) && (nds > 0)
? max(nas, nds) * (32 * 2 + 8)
: nas * 32 * 2 + nds * 8)),
nadc(32), sc_width(25), sc_height(200), aSamples(nas),
dSamples(nds) {
int off = sizeof(sls_detector_header);
cout << "hh" << dataSize << endl;
cout << sizeof(sls_detector_header) +
((nas > 0) && (nds > 0) ? max(nas, nds) * (32 * 2 + 8)
: nas * 32 * 2 + nds * 8)
<< endl;
nadc(32), sc_width(25), sc_height(200), aSamples(nas), dSamples(nds) {
#ifdef RAWDATA
off=sizeof(slsDetectorDefs::sls_receiver_header);
#endif
#ifndef RAWDATA
#ifndef CTB
off=sizeof(int);
#endif
#ifdef CTB
off=0;
#endif
#endif
/* int ds; */
/* if (nas && nds) */
/* if (nds>nas) */
/* ds=nds*(32*2+8); */
/* else */
/* ds=nas*(32*2+8); */
/* else */
/* ds=nas*32*2+nds*8; */
/* new slsDetectorData<uint16_t>(400, 400, ds); */
cout << "off is " << off << endl;
if (off>0)
cout << "M04 RAW DATA NEW " << endl;
else
cout << "M04 ZMQ DATA NEW " << endl;
int adc_nr[32] = {9, 8, 11, 10, 13, 12, 15, 14, 1, 0, 3,
2, 5, 4, 7, 6, 23, 22, 21, 20, 19, 18,
17, 16, 31, 30, 29, 28, 27, 26, 25, 24};
/*
iadc=ptr%32
isample=ptr/32
col=(adc_nr[iadc]%16)*25+isample%25
if (adc_nr[iadc]<16)
row=199-isample/25;
else
row=200+isample/25
adc0 col(9*25..10*25-1) row(199..0)
adc1 col(8*25..9*25-1) row(199..0)
adc2 col(11*25..12*25-1) row(199..0)
adc3 col(10*25..11*25-1) row(199..0)
adc4 col(13*25..14*25-1) row(199..0)
adc5 col(12*25..13*25-1) row(199..0)
adc6 col(15*25..16*25-1) row(199..0)
adc7 col(14*25..15*25-1) row(199..0)
adc8 col(1*25..2*25-1) row(199..0)
*/
int row, col;
@ -168,39 +100,11 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
}
}
/* for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){ */
/* xmap[ibyte]=-1; */
/* ymap[ibyte]=-1; */
/* } */
/* int off=sizeof(sls_detector_header)/2; */
/* for (ibyte=0; ibyte<dataSize; ibyte++) { */
/* for (ipacket=0; ipacket<npackets; ipacket++) { */
/* for (ibyte=0; ibyte< 8192/2; ibyte++) { */
/* i=ipacket*8208/2+ibyte; */
/* isample=ii/nadc; */
/* if (isample<nSamples) { */
/* iadc=ii%nadc; */
/* adc4 = (int)iadc/4; */
/* ix=isample%sc_width; */
/* iy=isample/sc_width; */
/* if (adc4%2==0) { */
/* xmap[i+off]=adc_nr[iadc]+ix; */
/* ymap[i+off]=ny/2-1-iy; */
/* } else { */
/* xmap[i+off]=adc_nr[iadc]+ix; */
/* ymap[i+off]=ny/2+iy; */
/* } */
/* } */
/* ii++; */
/* // } */
/* } */
/* } */
iframe = 0;
// cout << "data struct created" << endl;
}
}
int getGain(char *data, int x, int y) {
// int aoff=aSamples*2*32;
@ -253,10 +157,12 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
/* unsigned char bunchid[8]; */
/* }; */
#ifdef RAWDATA
int getFrameNumber(char *buff) {
return ((sls_detector_header *)buff)->frameNumber;
}; //*((int*)(buff+5))&0xffffff;};
#ifdef RAWDATA
return ((slsDetectorDefs::sls_receiver_header *)buff)->detHeader.frameNumber;
#endif
return (int)(*buff);
};
/**
@ -268,76 +174,15 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
*/
int getPacketNumber(char *buff) {
return ((sls_detector_header *)buff)->packetNumber;
} //((*(((int*)(buff+4))))&0xff)+1;};
#ifdef RAWDATA
return ((slsDetectorDefs::sls_receiver_header *)buff)->detHeader.packetNumber;
#endif
#ifndef RAWDATA
int getFrameNumber(char *buff) {
return iframe;
}; //((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};
#endif
/**
Returns the packet number for the given dataset. purely virtual func
\param buff pointer to the dataset
\returns packet number number
return 0;
}
*/
// int getPacketNumber(char *buff){return
// ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};
/* /\** */
/* Loops over a memory slot until a complete frame is found (i.e.
* all packets 0 to nPackets, same frame number). purely virtual func */
/* \param data pointer to the memory to be analyzed */
/* \param ndata reference to the amount of data found for the
* frame, in case the frame is incomplete at the end of the memory slot
*/
/* \param dsize size of the memory slot to be analyzed */
/* \returns pointer to the beginning of the last good frame (might
* be incomplete if ndata smaller than dataSize), or NULL if no frame is
* found */
/* *\/ */
/* virtual char *findNextFrame(char *data, int &ndata, int
* dsize){ndata=dsize; setDataSize(dsize); return data;}; */
/* /\** */
/* Loops over a file stream until a complete frame is found (i.e.
* all packets 0 to nPackets, same frame number). Can be overloaded for
* different kind of detectors! */
/* \param filebin input file stream (binary) */
/* \returns pointer to the begin of the last good frame, NULL if no
* frame is found or last frame is incomplete */
/* *\/ */
/* virtual char *readNextFrame(ifstream &filebin){ */
/* // int afifo_length=0; */
/* uint16_t *afifo_cont; */
/* int ib=0; */
/* if (filebin.is_open()) { */
/* afifo_cont=new uint16_t[dataSize/2]; */
/* while (filebin.read(((char*)afifo_cont)+ib,2)) { */
/* ib+=2; */
/* if (ib==dataSize) break; */
/* } */
/* if (ib>0) { */
/* iframe++; */
/* // cout << ib << "-" << endl; */
/* return (char*)afifo_cont; */
/* } else { */
/* delete [] afifo_cont; */
/* return NULL; */
/* } */
/* } */
/* return NULL; */
/* }; */
virtual char *readNextFrame(ifstream & filebin) {
int ff = -1, np = -1;
return readNextFrame(filebin, ff, np);
@ -358,11 +203,12 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
return data;
}
#ifndef RAWDATA
virtual char *readNextFrame(ifstream & filebin, int &ff, int &np,
char *data) {
// char *retval=0;
#ifndef RAWDATA
// int nd;
// int fnum = -1;
np = 0;
@ -380,19 +226,13 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
}
}
return NULL;
};
#endif
#ifdef RAWDATA
virtual char *readNextFrame(ifstream & filebin, int &ff, int &np,
char *data) {
char *retval = 0;
int nd;
//int nd;
int fnum = -1;
np = 0;
int pn;
//int pn;
// cout << dataSize << endl;
if (ff >= 0)
@ -406,9 +246,9 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
}
}
return NULL;
};
#endif
};
/**
@ -433,3 +273,4 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
};
#endif

216
slsDetectorCalibration/dataStructures/moenchData.h Normal file
View File

@ -0,0 +1,216 @@
// SPDX-License-Identifier: LGPL-3.0-or-other
// Copyright (C) 2021 Contributors to the SLS Detector Package
#ifndef MOENCHDATA_H
#define MOENCHDATA_H
#include "slsDetectorData.h"
#include "sls/sls_detector_defs.h"
using namespace std;
class moenchData : public slsDetectorData<uint16_t> {
private:
int iframe;
int nadc;
int sc_width;
int sc_height;
const int aSamples;
const int dSamples;
int off;
int *adc_nr;
int *ibit;
public:
/**
Implements the slsReceiverData structure for the moench02 prototype read
out by a module i.e. using the slsReceiver (160x160 pixels, 40 packets
1286 large etc.) \param c crosstalk parameter for the output buffer
*/
moenchData(int off, int nadc_i, int *adc_nr_in, int *ibit_in, int nas = 5000, int nds = 0, int nx_i=400, int ny_i=400)
: nadc(nadc_i), slsDetectorData<uint16_t>(nx_i, ny_i,off+((nas > 0) && (nds > 0)
? max(nas, nds) * (nadc_i * 2 + 8)
: nas * nadc_i * 2 + nds * 8)),
sc_width(25), sc_height(200), aSamples(nas), dSamples(nds) {
adc_nr=new int[nadc];
if (ibit_in)
ibit=new int[nadc];
else
ibit=NULL;
for (iadc=0; iadc<nadc; iadc++) {
adc_nr[iadc]=adc_nr_in[iadc];
if (ibit)
ibit[iadc]=ibit_in[iadc];
}
int row, col;
int iadc;
int i;
for (int is = 0; is < aSamples; is++) {
for (iadc = 0; iadc < nadc; iadc++) {
i = is;
// adc4=(int)iadc/4;
if (i < sc_width * sc_height) {
// for (int i=0; i<sc_width*sc_height; i++) {
col = (adc_nr[iadc] % 16) * sc_width + (i % sc_width);
// if (adc4%2==0) {
if (iadc < 16) {
row = 199 - i / sc_width;
} else {
row = 200 + i / sc_width;
}
if (nds > 0)
dataMap[row][col] =
((nadc + 4) * i + iadc) * 2 + off; //+16*(ip+1);
else
dataMap[row][col] =
(nadc * i + iadc) * 2 + off; //+16*(ip+1);
if (dataMap[row][col] < 0 ||
dataMap[row][col] >= aSamples * 2 * 32 + off)
cout << "Error: pointer " << dataMap[row][col]
<< " out of range " << endl;
}
}
}
iframe = 0;
}
virtual int getGain(char *data, int x, int y) {
// int aoff=aSamples*2*32;
if (ibit) {
int irow;
int isc = x / sc_width;
int icol = x % sc_width;
if (y < 200)
irow = sc_height - 1 - y;
else {
irow = y - sc_height;
isc++;
}
int isample = irow * sc_width + icol;
uint64_t sample;
char *ptr;
if (isc < 0 || isc >= 32)
return 0;
if (ibit[isc] < 0 || ibit[isc] >= 64)
return 0;
if (dSamples > isample) {
ptr = data + 32 * (isample + 1) + 8 * isample;
sample = *((uint64_t *)ptr);
if (sample & (1 << ibit[isc]))
return 1;
}
}
return 0;
}
/**
Returns the frame number for the given dataset. Purely virtual func.
\param buff pointer to the dataset
\returns frame number
*/
int getFrameNumber(char *buff) {
return (int* buff)[0];
};
/**
Returns the packet number for the given dataset. purely virtual func
\param buff pointer to the dataset
\returns packet number number
*/
int getPacketNumber(char *buff) {
return 0;
}
virtual char *readNextFrame(ifstream & filebin) {
int ff = -1, np = -1;
return readNextFrame(filebin, ff, np);
};
virtual char *readNextFrame(ifstream & filebin, int &ff) {
int np = -1;
return readNextFrame(filebin, ff, np);
};
virtual char *readNextFrame(ifstream & filebin, int &ff, int &np) {
char *data = new char[dataSize];
char *d = readNextFrame(filebin, ff, np, data);
if (d == NULL) {
delete[] data;
data = NULL;
}
return data;
}
virtual char *readNextFrame(ifstream & filebin, int &ff, int &np,
char *data) {
char *retval = 0;
int nd;
int fnum = -1;
np = 0;
int pn;
// cout << dataSize << endl;
//if (ff >= 0)
// fnum = ff;
if (filebin.is_open()) {
if (filebin.read(data, dataSize)) {
ff = getFrameNumber(data);
np = getPacketNumber(data);
return data;
}
}
return NULL;
};
/**
Loops over a memory slot until a complete frame is found (i.e. all
packets 0 to nPackets, same frame number). purely virtual func \param
data pointer to the memory to be analyzed \param ndata reference to
the amount of data found for the frame, in case the frame is
incomplete at the end of the memory slot \param dsize size of the
memory slot to be analyzed \returns pointer to the beginning of the
last good frame (might be incomplete if ndata smaller than dataSize),
or NULL if no frame is found
*/
virtual char *findNextFrame(char *data, int &ndata, int dsize) {
if (dsize < dataSize)
ndata = dsize;
else
ndata = dataSize;
return data;
}
};
#endif

5
slsDetectorCalibration/dataStructures/slsDetectorData.h
View File

@ -4,11 +4,8 @@
#define SLSDETECTORDATA_H
#include <fstream>
#include <inttypes.h>
#include <iostream>
using namespace std;
template <class dataType> class slsDetectorData {
protected:
@ -369,7 +366,7 @@ template <class dataType> class slsDetectorData {
is incomplete
*/
virtual char *readNextFrame(ifstream &filebin) = 0;
virtual char *readNextFrame(std::ifstream &filebin) = 0;
};
#endif