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

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* 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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247
slsDetectorCalibration/dataStructures/moench04CtbZmq10GbData.h
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@ -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