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Read in art products for wire-cell imaging #36

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Read in art products for wire-cell imaging #36

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6273388
Read in art products for wire-cell imaging
ebelchio12 Aug 31, 2023
e49aec5
Update CookedFrameSource.cxx
ebelchio12 Sep 6, 2023
7307fa6
Update CookedFrameSource.cxx
ebelchio12 Sep 6, 2023
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275 changes: 237 additions & 38 deletions larwirecell/Components/CookedFrameSource.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
#include "WireCellAux/SimpleFrame.h"
#include "WireCellAux/SimpleTrace.h"
#include "WireCellUtil/NamedFactory.h"
#include "WireCellUtil/Waveform.h"

WIRECELL_FACTORY(wclsCookedFrameSource,
wcls::CookedFrameSource,
Expand All @@ -21,7 +22,7 @@ using namespace WireCell;
using WireCell::Aux::SimpleFrame;
using WireCell::Aux::SimpleTrace;

CookedFrameSource::CookedFrameSource() : m_nticks(0) {}
CookedFrameSource::CookedFrameSource() : m_nticks(0), l(Log::logger("io")) {}

CookedFrameSource::~CookedFrameSource() {}

Expand All @@ -32,22 +33,76 @@ WireCell::Configuration CookedFrameSource::default_configuration() const
cfg["tick"] = 0.5 * WireCell::units::us;
cfg["frame_tags"][0] = "orig"; // the tags to apply to this frame
cfg["nticks"] = m_nticks; // if nonzero, truncate or zero-pad frame to this number of ticks.

// ----- Ewerton: Modify original CookedFrameSource
// ----- to read in products for wire-cell imaging

cfg["wiener_inputTag"] = ""; // art tag for wiener recob::Wire
cfg["gauss_inputTag"] = ""; // art tag for gauss recob::Wire
Comment on lines +40 to +41
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I'll just make one big comment but it applies to essentially this whole diff.

There are two main problems with this PR that must be cleaned up. They are like we discussed on zoom and I commented on in the PR.

  1. This class must work for a wide variety of users and so should not have any application specific information that is hard-wired in C++ or in configuration. Ie, there should be no configuration keys nor C++ symbols that include the label wiener or bad, etc. Instead, the C++ should be purely "data driven" by the configuration.

  2. There should be no "modal" true/false configuration values. Instead, if some action is to be taken by the class then the configuration values needed to perform that action will be given. If no such configuration values are given then the class simply does not take the action.

Specifically:

  • Remove all the *_inputTag configuration and code that touches them. There is already a frame_tags configuration and that is generic and is interpreted by converting art::Event data into frame traces.

  • Remove the current cmm_tag (and badmasks_inputTag) configuration and all code that touches them. What the user must supply is a instead mapping that associates a CMM key (eg "bad" to an art::Event label. I would call this configuration parameter, perhaps, cmm_entries.

  • Remove m_cmm_setup and instead convert CMM information (using your existing by iterating on the new cmm_entries configuration. If that configuration is empty then so is the loop body. The actual conversion code you have at the end of this diff (the loop over bad_masks, but again, the symbol "bad" is ... bad) looks okay to me.

cfg["badmasks_inputTag"] = Json::arrayValue; // list of art tags for bad channels
cfg["threshold_inputTag"] = ""; // art tag for thresholds
cfg["cmm_tag"] = ""; // for now use a single tag for output cmm
return cfg;
}

void CookedFrameSource::configure(const WireCell::Configuration& cfg)
{
const std::string art_tag = cfg["art_tag"].asString();
if (art_tag.empty()) {
THROW(ValueError() << errmsg{"WireCell::CookedFrameSource requires a source_label"});
}
m_inputTag = cfg["art_tag"].asString();

m_tick = cfg["tick"].asDouble();
for (auto jtag : cfg["frame_tags"]) {
m_frame_tags.push_back(jtag.asString());
}
m_nticks = get(cfg, "nticks", m_nticks);

// check setup to be used
m_wiener_inputTag = cfg["wiener_inputTag"].asString();
m_gauss_inputTag = cfg["gauss_inputTag"].asString();
for (auto badmask : cfg["badmasks_inputTag"]) {
m_badmasks_inputTag.push_back(badmask.asString());
}
m_threshold_inputTag = cfg["threshold_inputTag"].asString();
m_cmm_tag = cfg["cmm_tag"].asString();

if (m_wiener_inputTag.empty() && m_gauss_inputTag.empty() && !m_badmasks_inputTag.size() &&
m_threshold_inputTag.empty() && m_cmm_tag.empty()) { // use standard setup
l->debug("wcls::CookedFrameSource: using standard setup");
m_cmm_setup = false;
}
else { // use cmm setup
l->debug("wcls::CookedFrameSource: using cmm setup");
m_cmm_setup = true;
}

if (!m_cmm_setup) {
const std::string art_tag = cfg["art_tag"].asString();
if (art_tag.empty()) {
THROW(ValueError() << errmsg{"wcls::CookedFrameSource requires a source_label"});
}
m_inputTag = cfg["art_tag"].asString();
}
else {
if (m_wiener_inputTag.empty())
THROW(ValueError() << errmsg{
"wcls::CookedFrameSource requires a source_label for recob::Wire (wiener)"});
if (m_gauss_inputTag.empty())
THROW(ValueError() << errmsg{
"wcls::CookedFrameSource requires a source_label for recob::Wire (gauss)"});
if (m_badmasks_inputTag.size()) {
for (auto badmask : m_badmasks_inputTag) {
if (badmask.empty())
THROW(ValueError() << errmsg{
"wcls::CookedFrameSource cannot use an empty source_label for bad masks"});
}
}
else {
THROW(
ValueError() << errmsg{"wcls::CookedFrameSource requires a source_label for bad masks"});
}
if (m_threshold_inputTag.empty())
THROW(
ValueError() << errmsg{"wcls::CookedFrameSource requires a source_label for threshold"});
if (m_cmm_tag.empty())
THROW(ValueError() << errmsg{"wcls::CookedFrameSource requires a label for cmm_tag"});
}
}

// this code assumes that the high part of timestamp represents number of seconds from Jan 1st, 1970 and the low part
Expand Down Expand Up @@ -89,43 +144,187 @@ void CookedFrameSource::visit(art::Event& e)
auto const& event = e;
// fixme: want to avoid depending on DetectorPropertiesService for now.
const double tick = m_tick;
art::Handle<std::vector<recob::Wire>> rwvh;
bool okay = event.getByLabel(m_inputTag, rwvh);
if (!okay) {
std::string msg =
"WireCell::CookedFrameSource failed to get vector<recob::Wire>: " + m_inputTag.encode();
std::cerr << msg << std::endl;
THROW(RuntimeError() << errmsg{msg});
const double time = tdiff(event.getRun().beginTime(), event.time());
if (!m_cmm_setup) { // do standard setup
art::Handle<std::vector<recob::Wire>> rwvh;
bool okay = event.getByLabel(m_inputTag, rwvh);
if (!okay) {
std::string msg =
"WireCell::CookedFrameSource failed to get vector<recob::Wire>: " + m_inputTag.encode();
std::cerr << msg << std::endl;
THROW(RuntimeError() << errmsg{msg});
}
else if (rwvh->size() == 0)
return;

const std::vector<recob::Wire>& rwv(*rwvh);
const size_t nchannels = rwv.size();
std::cerr << "CookedFrameSource: got " << nchannels << " recob::Wire objects\n";

WireCell::ITrace::vector traces(nchannels);
for (size_t ind = 0; ind < nchannels; ++ind) {
auto const& rw = rwv.at(ind);
traces[ind] = ITrace::pointer(make_trace(rw, m_nticks));
if (!ind) { // first time through
if (m_nticks) {
std::cerr << "\tinput nticks=" << rw.NSignal() << " setting to " << m_nticks << std::endl;
}
else {
std::cerr << "\tinput nticks=" << rw.NSignal() << " keeping as is" << std::endl;
}
}
}

auto sframe = new SimpleFrame(event.event(), time, traces, tick);
for (auto tag : m_frame_tags) {
//std::cerr << "\ttagged: " << tag << std::endl;
sframe->tag_frame(tag);
}
m_frames.push_back(WireCell::IFrame::pointer(sframe));
//m_frames.push_back(nullptr); //<- passes empty frame to next module?
}
else if (rwvh->size() == 0)
return;

const std::vector<recob::Wire>& rwv(*rwvh);
const size_t nchannels = rwv.size();
std::cerr << "CookedFrameSource: got " << nchannels << " recob::Wire objects\n";

WireCell::ITrace::vector traces(nchannels);
for (size_t ind = 0; ind < nchannels; ++ind) {
auto const& rw = rwv.at(ind);
traces[ind] = ITrace::pointer(make_trace(rw, m_nticks));
if (!ind) { // first time through
if (m_nticks) {
std::cerr << "\tinput nticks=" << rw.NSignal() << " setting to " << m_nticks << std::endl;
else { // do cmm setup

art::Handle<std::vector<recob::Wire>> rwvh_wiener;
art::Handle<std::vector<recob::Wire>> rwvh_gauss;
std::map<std::string, art::Handle<std::vector<int>>> bad_masks;
art::Handle<std::vector<double>> threshold;
bool okay_wiener = event.getByLabel(m_wiener_inputTag, rwvh_wiener);
bool okay_gauss = event.getByLabel(m_gauss_inputTag, rwvh_gauss);
for (auto badmask : m_badmasks_inputTag) {
bool okay = e.getByLabel(badmask, bad_masks[badmask.label()]);
if (!okay) {
std::string msg = "wcls::CookedFrameSource failed to get vector<int>: " + badmask.encode() +
" (badmask not found)";
std::cerr << msg << std::endl;
THROW(RuntimeError() << errmsg{msg});
}
else {
std::cerr << "\tinput nticks=" << rw.NSignal() << " keeping as is" << std::endl;
else if (bad_masks[badmask.label()]->size() == 0) {
std::string msg = "wcls::CookedFrameSource bad mask " + badmask.encode() + " is empty";
std::cerr << msg << std::endl;
return;
}
}
}
bool okay_th = e.getByLabel(m_threshold_inputTag, threshold);

const double time = tdiff(event.getRun().beginTime(), event.time());
auto sframe = new SimpleFrame(event.event(), time, traces, tick);
for (auto tag : m_frame_tags) {
//std::cerr << "\ttagged: " << tag << std::endl;
sframe->tag_frame(tag);
if (!okay_wiener) {
std::string msg =
"wcls::CookedFrameSource failed to get vector<recob::Wire>: " + m_wiener_inputTag.encode() +
" (wire-cell imaging needs both wiener and gauss recob::Wire)";
std::cerr << msg << std::endl;
THROW(RuntimeError() << errmsg{msg});
}
else if (rwvh_wiener->size() == 0)
return;

if (!okay_gauss) {
std::string msg =
"wcls::CookedFrameSource failed to get vector<recob::Wire>: " + m_gauss_inputTag.encode() +
" (wire-cell imaging needs both wiener and gauss recob::Wire)";
std::cerr << msg << std::endl;
THROW(RuntimeError() << errmsg{msg});
}
else if (rwvh_gauss->size() == 0)
return;

if (!okay_th) {
std::string msg =
"wcls::CookedFrameSource failed to get vector<double>: " + m_threshold_inputTag.encode() +
" (wire-cell imaging needs thresholds)";
std::cerr << msg << std::endl;
THROW(RuntimeError() << errmsg{msg});
}
else if (threshold->size() == 0)
return;

const std::vector<recob::Wire>& wiener_rwv(*rwvh_wiener);
const std::vector<recob::Wire>& gauss_rwv(*rwvh_gauss);
const size_t nchannels_wiener = wiener_rwv.size();
const size_t nchannels_gauss = gauss_rwv.size();
l->debug("wcls::CookedFrameSource: got {} (wiener) recob::Wire objects", nchannels_wiener);
l->debug("wcls::CookedFrameSource: got {} (gauss) recob::Wire objects", nchannels_gauss);

ITrace::vector* itraces = new ITrace::vector; // will become shared_ptr.
IFrame::trace_list_t indices;
IFrame::trace_list_t wiener_traces, gauss_traces;

for (size_t ind = 0; ind < nchannels_wiener; ++ind) {
auto const& rw = wiener_rwv.at(ind);
SimpleTrace* trace = make_trace(rw, m_nticks);
const size_t trace_index = itraces->size();

indices.push_back(trace_index);
wiener_traces.push_back(trace_index);
itraces->push_back(ITrace::pointer(trace));

if (!ind) { // first time through
if (m_nticks) {
l->debug("wcls::CookedFrameSource: input nticks= {} setting to {} (wiener)",
rw.NSignal(),
m_nticks);
}
else {
l->debug("wcls::CookedFrameSource: input nticks= {} keeping as is (wiener)",
rw.NSignal());
}
}
}

for (size_t ind = 0; ind < nchannels_gauss; ++ind) {
auto const& rw = gauss_rwv.at(ind);
SimpleTrace* trace = make_trace(rw, m_nticks);
const size_t trace_index = itraces->size();

indices.push_back(trace_index);
gauss_traces.push_back(trace_index);
itraces->push_back(ITrace::pointer(trace));

if (!ind) { // first time through
if (m_nticks) {
l->debug("wcls::CookedFrameSource: input nticks= {} setting to {} (gauss)\n",
rw.NSignal(),
m_nticks);
}
else {
l->debug("wcls::CookedFrameSource: input nticks= {} keeping as is (gauss)\n",
rw.NSignal());
}
}
}

Waveform::ChannelMaskMap cmm;
Waveform::ChannelMasks cm_out;

for (auto bad_mask : bad_masks) {
Waveform::ChannelMasks cm;
size_t nchannels = bad_mask.second->size() / 3;
for (size_t i = 0; i < nchannels; i++) {
size_t ch_idx = 3 * i;
size_t low_idx = 3 * i + 1;
size_t up_idx = 3 * i + 2;
auto cmch = bad_mask.second->at(ch_idx);
auto cm_first = bad_mask.second->at(low_idx);
auto cm_second = bad_mask.second->at(up_idx);
Waveform::BinRange bins(cm_first, cm_second);
cm[cmch].push_back(bins);
}
cm_out = Waveform::merge(cm_out, cm);
}

cmm[m_cmm_tag] = cm_out; // for now use a single tag for output cmm
Comment on lines +298 to +314
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I think this is mostly okay but do not use the symbol bad and save into the cmm using the key from the cmm_entries configuration and not any singular name (ie, remove m_cmm_tag entirely).


auto sframe =
new Aux::SimpleFrame(event.event(), time, ITrace::shared_vector(itraces), tick, cmm);
for (auto tag : m_frame_tags) {
sframe->tag_frame(tag);
}

sframe->tag_traces(m_wiener_tag, wiener_traces, *threshold);
sframe->tag_traces(m_gauss_tag, gauss_traces);

m_frames.push_back(WireCell::IFrame::pointer(sframe));
//m_frames.push_back(nullptr); //<- passes empty frame to next module?
}
m_frames.push_back(WireCell::IFrame::pointer(sframe));
m_frames.push_back(nullptr);
}

bool CookedFrameSource::operator()(WireCell::IFrame::pointer& frame)
Expand Down