summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorBrian Helfrich <helfrich9000@gmail.com>2008-01-29 01:15:46 +0000
committerBrian Helfrich <helfrich9000@gmail.com>2008-01-29 01:15:46 +0000
commit0c1762a6afba84ccd01aef8c51cb7aae734a8d1e (patch)
treed9bc4f9158355e3b8ffdb01b00aeb244676f1702
parentd5434222bf82fa95a8a5279d610924c6019a8bd9 (diff)
downloadnanoengineer-0c1762a6afba84ccd01aef8c51cb7aae734a8d1e.tar.gz
nanoengineer-0c1762a6afba84ccd01aef8c51cb7aae734a8d1e.zip
Now handles data stores that are still being written to.
Diffstat
-rw-r--r--cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataImportExportPlugin.h3
-rw-r--r--cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataStoreInfo.h5
-rw-r--r--cad/plugins/NanoVision-1/include/Nanorex/Interface/NXEntityManager.h18
-rw-r--r--cad/plugins/NanoVision-1/src/Interface/NXEntityManager.cpp59
-rw-r--r--cad/plugins/NanoVision-1/src/KDevelop/Testing/HDF5_Consumer/HDF5_Consumer.pro16
-rw-r--r--cad/plugins/NanoVision-1/src/KDevelop/Testing/Testing.pro3
-rw-r--r--cad/plugins/NanoVision-1/src/KDevelop/nv1.kdevelop9
-rw-r--r--cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExport.cpp15
-rw-r--r--cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExportTest.cpp2
-rw-r--r--cad/plugins/NanoVision-1/src/Testing/HDF5_Consumer/HDF5_Consumer.cpp108
10 files changed, 216 insertions, 22 deletions
diff --git a/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataImportExportPlugin.h b/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataImportExportPlugin.h
index d80556c79..891fd811b 100644
--- a/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataImportExportPlugin.h
+++ b/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataImportExportPlugin.h
@@ -53,6 +53,9 @@ class NXDataImportExportPlugin : public NXPlugin {
* handle from dataStoreInfo. If opening a multi-frame file, a handle
* to it will be stored in the dataStoreInfo for later use (subsequent
* importFromFile calls.)
+ *
+ * No modifications to the given moleculeSet will result in deletion
+ * of the frame with the given frameIndex.
*/
virtual NXCommandResult* importFromFile
(NXMoleculeSet* moleculeSet, NXDataStoreInfo* dataStoreInfo,
diff --git a/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataStoreInfo.h b/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataStoreInfo.h
index 6d4a34ede..326735adf 100644
--- a/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataStoreInfo.h
+++ b/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXDataStoreInfo.h
@@ -20,6 +20,9 @@ class NXDataStoreInfo {
public:
NXDataStoreInfo() { }
+ const string& getFilename() { return _filename; }
+ void setFilename(const string& filename) { _filename = filename; }
+
void addTrajectory(string name, int id) { _trajectories[name] = id; }
int getTrajectoryId(string name) { return _trajectories[name]; }
//vector<string> getTrajectoryNames();
@@ -38,6 +41,8 @@ class NXDataStoreInfo {
void* getHandle(int id) { return _handle[id]; }
private:
+ string _filename;
+
// Maps trajectory name to its frame set id.
map<string, int> _trajectories;
diff --git a/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXEntityManager.h b/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXEntityManager.h
index 68901e4e5..d9c305495 100644
--- a/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXEntityManager.h
+++ b/cad/plugins/NanoVision-1/include/Nanorex/Interface/NXEntityManager.h
@@ -36,11 +36,12 @@ class NXEntityManager {
// Import/export plugins
//
void loadDataImportExportPlugins(NXProperties* properties);
- NXCommandResult* importFromFile(const string& filename);
+ NXCommandResult* importFromFile(const string& filename,
+ int frameSetId = -1, int frameIndex = 0);
NXCommandResult* exportToFile(const string& filename,
int frameSetId = -1, int frameIndex = 0);
- const NXDataStoreInfo* getDataStoreInfo() { return dataStoreInfo; }
+ NXDataStoreInfo* getDataStoreInfo() { return dataStoreInfo; }
//
// Frame sets
@@ -55,18 +56,13 @@ class NXEntityManager {
moleculeSets[frameSetId].push_back(moleculeSet);
return moleculeSets[frameSetId].size() - 1;
}
+ void removeLastFrame(int frameSetId) {
+ moleculeSets[frameSetId].pop_back();
+ }
unsigned int getFrameCount(int frameSetId) {
return moleculeSets[frameSetId].size();
}
- NXMoleculeSet* getRootMoleculeSet(int frameSetId, int frameIndex = 0) {
- if (frameIndex < (int)moleculeSets[frameSetId].size())
- return moleculeSets[frameSetId][frameIndex];
- else {
- // See if there's a new frame
- // or
- return 0;
- }
- }
+ NXMoleculeSet* getRootMoleculeSet(int frameSetId, int frameIndex);
private:
NXPluginGroup* dataImpExpPluginGroup;
diff --git a/cad/plugins/NanoVision-1/src/Interface/NXEntityManager.cpp b/cad/plugins/NanoVision-1/src/Interface/NXEntityManager.cpp
index 8386cf923..101c46d23 100644
--- a/cad/plugins/NanoVision-1/src/Interface/NXEntityManager.cpp
+++ b/cad/plugins/NanoVision-1/src/Interface/NXEntityManager.cpp
@@ -124,19 +124,32 @@ void NXEntityManager::loadDataImportExportPlugins(NXProperties* properties) {
/* FUNCTION: importFromFile */
-NXCommandResult* NXEntityManager::importFromFile(const string& filename) {
+/**
+ * @param frameSetId If -1, import everything, otherwise, resume importing
+ * the frame set from the given frameIndex.
+ */
+NXCommandResult* NXEntityManager::importFromFile(const string& filename,
+ int frameSetId,
+ int frameIndex) {
NXCommandResult* result;
//PR_Lock(importExportPluginsMutex);
+ dataStoreInfo->setFilename(filename);
string fileType = getFileType(filename);
map<string, NXDataImportExportPlugin*>::iterator iter =
dataImportTable.find(fileType);
if (iter != dataImportTable.end()) {
NXDataImportExportPlugin* plugin = iter->second;
- int frameSetId = addFrameSet();
- int frameIndex = addFrame(frameSetId);
+
+ if (frameSetId == -1) {
+ frameSetId = addFrameSet();
+ frameIndex = addFrame(frameSetId);
+
+ } else {
+ frameIndex = addFrame(frameSetId);
+ }
try {
plugin->setMode(fileType);
@@ -145,8 +158,16 @@ NXCommandResult* NXEntityManager::importFromFile(const string& filename) {
frameIndex),
dataStoreInfo, filename, frameSetId,
frameIndex);
+
if (result->getResult() == NX_CMD_SUCCESS) {
+ // Delete the frame if the molecule set wasn't populated.
+ NXMoleculeSet* moleculeSet =
+ getRootMoleculeSet(frameSetId, frameIndex);
+ if ((moleculeSet->childCount() == 0) &&
+ (moleculeSet->moleculeCount() == 0))
+ removeLastFrame(frameSetId);
+
// TODO:
// Finish the current frame set, then examine the dataStoreInfo
// for additional files to import.
@@ -160,9 +181,12 @@ NXCommandResult* NXEntityManager::importFromFile(const string& filename) {
dataStoreInfo, filename,
frameSetId, frameIndex);
}
- }
+ } else
+ removeLastFrame(frameSetId);
} catch (...) {
+ removeLastFrame(frameSetId);
+
string msg = fileType;
msg += "->importFromFile() threw exception";
NXLOG_SEVERE("NXEntityManager", msg);
@@ -234,7 +258,7 @@ NXCommandResult* NXEntityManager::exportToFile
dataStoreInfo->setLastFrame
(frameSetId,
!allFrameExport ||
- (frameIndex > (int)moleculeSets[frameSetId].size() - 2));
+ (frameIndex > (int)moleculeSets[frameSetId].size() - 2));
vector<NXMoleculeSet*>::iterator iter =
moleculeSets[frameSetId].begin();
result =
@@ -295,6 +319,31 @@ NXCommandResult* NXEntityManager::exportToFile
}
+/* FUNCTION: getRootMoleculeSet */
+NXMoleculeSet* NXEntityManager::getRootMoleculeSet(int frameSetId,
+ int frameIndex) {
+
+ if (frameIndex < (int)moleculeSets[frameSetId].size())
+ return moleculeSets[frameSetId][frameIndex];
+ else {
+ if (dataStoreInfo->storeIsComplete(frameSetId))
+ return 0;
+ else {
+ // See if there's a new frame
+ NXCommandResult* result =
+ importFromFile(dataStoreInfo->getFilename(),
+ frameSetId,
+ moleculeSets[frameSetId].size());
+ // TODO: Handle when result != 0
+ if (frameIndex < (int)moleculeSets[frameSetId].size())
+ return moleculeSets[frameSetId][frameIndex];
+ else
+ return 0;
+ }
+ }
+}
+
+
/* FUNCTION: getFileType */
string NXEntityManager::getFileType(const string& filename) {
int index = filename.rfind(".");
diff --git a/cad/plugins/NanoVision-1/src/KDevelop/Testing/HDF5_Consumer/HDF5_Consumer.pro b/cad/plugins/NanoVision-1/src/KDevelop/Testing/HDF5_Consumer/HDF5_Consumer.pro
new file mode 100644
index 000000000..69f0e4cfc
--- /dev/null
+++ b/cad/plugins/NanoVision-1/src/KDevelop/Testing/HDF5_Consumer/HDF5_Consumer.pro
@@ -0,0 +1,16 @@
+SOURCES += ../../../Testing/HDF5_Consumer/HDF5_Consumer.cpp
+
+TEMPLATE = app
+
+INCLUDEPATH += $(OPENBABEL_INCPATH) \
+../../../../include
+LIBS += -lopenbabel \
+-L../../../../lib \
+-lHDF5_SimResultsImportExport \
+-lNanorexInterface \
+-lNanorexUtility
+TARGETDEPS += ../../../../lib/libHDF5_SimResultsImportExport.so \
+../../../../lib/libNanorexInterface.so \
+../../../../lib/libNanorexUtility.so
+DESTDIR = ../../../../bin/
+
diff --git a/cad/plugins/NanoVision-1/src/KDevelop/Testing/Testing.pro b/cad/plugins/NanoVision-1/src/KDevelop/Testing/Testing.pro
index 7440d3dbc..385cf14ca 100644
--- a/cad/plugins/NanoVision-1/src/KDevelop/Testing/Testing.pro
+++ b/cad/plugins/NanoVision-1/src/KDevelop/Testing/Testing.pro
@@ -1,3 +1,4 @@
TEMPLATE = subdirs
-SUBDIRS += CppUnit
+SUBDIRS += CppUnit \
+ HDF5_Consumer
diff --git a/cad/plugins/NanoVision-1/src/KDevelop/nv1.kdevelop b/cad/plugins/NanoVision-1/src/KDevelop/nv1.kdevelop
index aa94916ce..a65ce27bb 100644
--- a/cad/plugins/NanoVision-1/src/KDevelop/nv1.kdevelop
+++ b/cad/plugins/NanoVision-1/src/KDevelop/nv1.kdevelop
@@ -156,21 +156,24 @@
<runarguments>
<HDF5_SimResultsImportExport/>
<GLT/>
- <CppUnit></CppUnit>
+ <CppUnit/>
+ <HDF5_Consumer/>
</runarguments>
<cwd>
<HDF5_SimResultsImportExport>/home/rmanoj/Nanorex/SVN/trunk/cad/plugins/NanoVision-1/src/KDevelop</HDF5_SimResultsImportExport>
<GLT>/home/rmanoj/Nanorex/SVN/trunk/cad/plugins/NanoVision-1/src/KDevelop</GLT>
<CppUnit>/home/bh/11Nano/SVN-D/cad/plugins/NanoVision-1/src/KDevelop/../../../..</CppUnit>
+ <HDF5_Consumer>/home/bh/11Nano/SVN-D/cad/plugins/NanoVision-1/src/KDevelop</HDF5_Consumer>
</cwd>
<debugarguments>
<HDF5_SimResultsImportExport/>
<GLT/>
- <CppUnit></CppUnit>
+ <CppUnit/>
+ <HDF5_Consumer/>
</debugarguments>
</run>
<general>
- <activedir>Testing/CppUnit</activedir>
+ <activedir>Testing</activedir>
</general>
<make>
<abortonerror>true</abortonerror>
diff --git a/cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExport.cpp b/cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExport.cpp
index 9f3887d86..5ec5ba8bd 100644
--- a/cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExport.cpp
+++ b/cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExport.cpp
@@ -51,6 +51,15 @@ NXCommandResult* HDF5_SimResultsImportExport::importFromFile
populateCommandResult(result, message.c_str());
}
+ simResults->synchronize();
+
+ // See if the requested frame exists (yet) and abort if it doesn't
+ // signaling to delete the frame for the given frameIndex.
+ int frameCount = 0;
+ simResults->getFrameCount("frame-set-1", frameCount);
+ if (frameCount == 0)
+ return result;
+
// If this is the first call to import the data store, retrieve the meta
// information about the data store, and other data.
if ((frameIndex == 0) && (frameSetId == 0) &&
@@ -82,7 +91,9 @@ NXCommandResult* HDF5_SimResultsImportExport::importFromFile
unsigned int atomIds[atomCount];
unsigned int atomicNumbers[atomCount];
float positions[atomCount*3];
- void* bonds = (void*)malloc(bondCount*sizeof(SimResultsBond));
+ void* bonds = 0;
+ if (bondCount != 0)
+ bonds = (void*)malloc(bondCount*sizeof(SimResultsBond));
// Retrieve atom data
if (result->getResult() == NX_CMD_SUCCESS) {
@@ -105,7 +116,7 @@ NXCommandResult* HDF5_SimResultsImportExport::importFromFile
}
// Retrieve bond data
- if (result->getResult() == NX_CMD_SUCCESS) {
+ if ((result->getResult() == NX_CMD_SUCCESS) && (bondCount != 0)) {
status = simResults->getFrameBonds("frame-set-1", 0, bonds, message);
if (status)
populateCommandResult(result, message.c_str());
diff --git a/cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExportTest.cpp b/cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExportTest.cpp
index 0f5b0e8c6..aa5c1e259 100644
--- a/cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExportTest.cpp
+++ b/cad/plugins/NanoVision-1/src/Plugins/HDF5_SimResultsImportExport/HDF5_SimResultsImportExportTest.cpp
@@ -76,10 +76,12 @@ void HDF5_SimResultsImportExportTest::basicExportTest() {
bond = molecule->NewBond();
bond->SetBegin(atomO);
bond->SetEnd(atomH2);
+printf("\n> 3\n");
// Write it with the HDF5_SimResultsImportExport plugin
NXCommandResult* commandResult =
entityManager->exportToFile("testHDF5store.nh5", frameSetId, -1);
+printf("> 4\n");
if (commandResult->getResult() != NX_CMD_SUCCESS)
printf("\n%s\n", qPrintable(GetNV1ResultCodeString(commandResult)));
CPPUNIT_ASSERT(commandResult->getResult() == NX_CMD_SUCCESS);
diff --git a/cad/plugins/NanoVision-1/src/Testing/HDF5_Consumer/HDF5_Consumer.cpp b/cad/plugins/NanoVision-1/src/Testing/HDF5_Consumer/HDF5_Consumer.cpp
new file mode 100644
index 000000000..ba41b91a7
--- /dev/null
+++ b/cad/plugins/NanoVision-1/src/Testing/HDF5_Consumer/HDF5_Consumer.cpp
@@ -0,0 +1,108 @@
+
+// Copyright 2008 Nanorex, Inc. See LICENSE file for details.
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <signal.h>
+#include <time.h>
+
+#include <string>
+
+#include "Nanorex/Interface/NXEntityManager.h"
+using namespace Nanorex;
+
+
+/* FUNCTION: set_timespec */
+void set_timespec(struct timespec *tmr, unsigned long long ustime) {
+ tmr->tv_sec = (time_t) (ustime / 1000000ULL);
+ tmr->tv_nsec = (long) (1000ULL * (ustime % 1000000ULL));
+}
+
+
+NXEntityManager* entityManager = 0;
+int trajId = 0;
+unsigned int frameIndex = 0;
+
+
+/* FUNCTION: render */
+void render(int dummy) {
+ NXMoleculeSet* moleculeSet =
+ entityManager->getRootMoleculeSet(trajId, frameIndex);
+ unsigned int frameCount = 0;
+ if (moleculeSet != 0) {
+ printf("\n==========================\n");
+ frameCount = entityManager->getFrameCount(trajId);
+ OBMolIterator moleculeIter = moleculeSet->moleculesBegin();
+ printf("%d ", (*moleculeIter)->GetAtom(1)->GetAtomicNum());
+ printf("%g ", (*moleculeIter)->GetAtom(1)->GetZ());
+ printf("%d ", (*moleculeIter)->NumBonds());
+ printf("frame:%d/%d\n", frameIndex+1, frameCount);
+
+ frameIndex++;
+ }
+}
+
+
+/* FUNCTION: main */
+int main(int argc, char* argv[]) {
+
+ // Set the entity manager up
+ //
+ entityManager = new NXEntityManager();
+
+ NXProperties* properties = new NXProperties();
+ properties->setProperty("NXEntityManager.importExport.0.plugin",
+ "libHDF5_SimResultsImportExport");
+ properties->setProperty("NXEntityManager.importExport.0.pluginConfigFile",
+ "../lib/HDF5_SimResultsImportExport.cfg");
+ entityManager->loadDataImportExportPlugins(properties);
+ delete properties;
+
+ // Prime read
+ NXCommandResult* commandResult =
+ entityManager->importFromFile("Testing/shared.nh5");
+ if (commandResult->getResult() != NX_CMD_SUCCESS) {
+ printf("%s\n", qPrintable(GetNV1ResultCodeString(commandResult)));
+ exit(1);
+ }
+
+ // Discover a store-not-complete trajectory frame set
+ NXDataStoreInfo* dataStoreInfo = entityManager->getDataStoreInfo();
+ trajId = dataStoreInfo->getTrajectoryId("frame-set-1");
+ if (dataStoreInfo->storeIsComplete(trajId)) {
+ printf("error: data store is complete\n");
+ exit(1);
+ }
+
+ // Set up a repeating timer and start it
+ timer_t timerid;
+ struct sigaction sigact;
+ struct sigevent sigev;
+ sigact.sa_handler = render;
+ sigemptyset(&(sigact.sa_mask));
+ sigact.sa_flags = 0;
+ if (sigaction(SIGUSR1, &sigact, (struct sigaction *)NULL) == -1) {
+ printf("sigaction failed");
+ exit(1);
+ }
+ sigev.sigev_notify = SIGEV_SIGNAL;
+ sigev.sigev_signo = SIGUSR1;
+ if (timer_create(CLOCK_REALTIME, &sigev, &timerid) == -1) {
+ printf("timer_create failed");
+ exit(1);
+ }
+ struct itimerspec tmr;
+ set_timespec(&tmr.it_value, 1000 * 1000); // 1000 milliseconds
+ //set_timespec(&tmr.it_value, 100 * 1000); // 100 milliseconds
+ set_timespec(&tmr.it_interval, 100 * 1000);
+ if (timer_settime(timerid, 0, &tmr, (struct itimerspec *)NULL) == -1) {
+ printf("timer_create failed");
+ exit(1);
+ }
+
+ while (!dataStoreInfo->storeIsComplete(trajId)) {
+ printf(" . "); fflush(0);
+ pause();
+ }
+ return 0;
+}
generated by cgit v1.2.3 (git 2.39.1) at 2025-05-04 06:59:49 +0000