Examples with FRAPStudy cbit.vcell.microscopy.FRAPStudy used on opensource projects

Example 26 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class FRAPBatchRunWorkspace method updateDisplayForTreeSelection.

public void updateDisplayForTreeSelection(Object selection) {
    String oldString = null;
    if (// doc
    displaySelection instanceof File) {
        oldString = ((File) displaySelection).getAbsolutePath();
    } else if (// results
    displaySelection instanceof String) {
        oldString = ((String) displaySelection);
    }
    displaySelection = selection;
    if (// doc
    selection instanceof File) {
        String newString = ((File) selection).getAbsolutePath();
        FRAPStudy selectedFrapStudy = getFRAPStudy(newString);
        setWorkingFRAPStudy(selectedFrapStudy);
        firePropertyChange(PROPERTY_CHANGE_BATCHRUN_DISPLAY_IMG, oldString, newString);
    } else if (// results
    selection instanceof String) {
        firePropertyChange(PROPERTY_CHANGE_BATCHRUN_DISPLAY_PARAM, oldString, (selection));
    }
}

Example 27 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class FRAPBatchRunWorkspace method addFrapStudy.

public void addFrapStudy(FRAPStudy newFrapStudy) {
    File newFile = new File(newFrapStudy.getXmlFilename());
    ArrayList<FRAPStudy> frapStudies = getFrapStudies();
    int size = frapStudies.size();
    int insertIdx = size;
    for (int i = 0; i < size; i++) {
        File xmlFile = new File(frapStudies.get(i).getXmlFilename());
        if (newFile.getName().compareTo(xmlFile.getName()) == 0) {
            if (newFile.getAbsolutePath().compareTo(xmlFile.getAbsolutePath()) < 0) {
                insertIdx = i;
                break;
            }
        } else if (newFile.getName().compareTo(xmlFile.getName()) < 0) {
            insertIdx = i;
            break;
        }
    }
    if (insertIdx == size) {
        frapStudies.add(newFrapStudy);
    } else {
        frapStudies.add(insertIdx, newFrapStudy);
    }
    // enable save button
    VirtualFrapBatchRunFrame.enableSave(frapStudies != null && frapStudies.size() > 0);
}

Example 28 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class FRAPBatchRunWorkspace method getSaveSingleFilesTask.

// get client task for saving single vfrap files
public AsynchClientTask getSaveSingleFilesTask() {
    AsynchClientTask saveSingleFileTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            int size = getFrapStudies().size();
            for (int i = 0; i < getFrapStudies().size(); i++) {
                FRAPStudy fStudy = getFrapStudies().get(i);
                File outFile = new File(fStudy.getXmlFilename());
                this.getClientTaskStatusSupport().setMessage("Saving file " + (i + 1) + " of " + size + " :" + outFile.getAbsolutePath() + " ...");
                saveProcedure(outFile, fStudy, this.getClientTaskStatusSupport());
            }
        }
    };
    return saveSingleFileTask;
}

Example 29 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class BatchRunDetailsPanel method actionPerformed.

public void actionPerformed(ActionEvent e) {
    Object source = e.getSource();
    if (source == addButton) {
        // check file before loading into batch run, if the file has .vfrap extension
        // check if it has the model that is required by the batch run, if no, run the reference simulation and get the parameters
        final Wizard loadWizard = getAddFRAPDataWizard();
        if (loadWizard != null) {
            loadWizard.showModalDialog(new Dimension(550, 640));
            // code return
            if (loadWizard.getReturnCode() == Wizard.FINISH_RETURN_CODE) {
                // get newly added frapstudy
                FRAPStudy fStudy = getBatchRunWorkspace().getWorkingFrapStudy();
                // check if the batch run has results already and the newly loaded data should have same model ready
                int batchRunSelectedModel = getBatchRunWorkspace().getSelectedModel();
                if (getBatchRunWorkspace().isBatchRunResultsAvailable() && fStudy.getModels()[batchRunSelectedModel] != null && fStudy.getFrapModel(batchRunSelectedModel).getModelParameters() != null) {
                    Parameter[] parameters = fStudy.getFrapModel(batchRunSelectedModel).getModelParameters();
                    double[][] fitData = null;
                    if (batchRunSelectedModel == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT || batchRunSelectedModel == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS) {
                        FRAPOptData optData = fStudy.getFrapOptData();
                        // newly loaded frapstudy doesn't have estimation data ready, generate the data
                        if (optData == null) {
                            try {
                                optData = new FRAPOptData(fStudy, parameters.length, getLocalWorkspace(), fStudy.getStoredRefData());
                                fStudy.setFrapOptData(optData);
                                fitData = optData.getFitData(parameters);
                            } catch (Exception ex) {
                                ex.printStackTrace(System.out);
                                DialogUtils.showErrorDialog(BatchRunDetailsPanel.this, ex.getMessage());
                            }
                        }
                    } else if (batchRunSelectedModel == FRAPModel.IDX_MODEL_REACTION_OFF_RATE) {
                        FRAPOptFunctions optFunc = fStudy.getFrapOptFunc();
                        if (optFunc == null) {
                            try {
                                optFunc = new FRAPOptFunctions(fStudy);
                                fStudy.setFrapOptFunc(optFunc);
                                fitData = optFunc.getFitData(parameters);
                            } catch (Exception ex2) {
                                ex2.printStackTrace();
                                DialogUtils.showErrorDialog(BatchRunDetailsPanel.this, ex2.getMessage());
                            }
                        }
                    }
                    fStudy.getModels()[batchRunSelectedModel].setData(fitData);
                    // add new data into the frapStudy list in batch run.
                    getBatchRunWorkspace().addFrapStudy(fStudy);
                    // refresh the results
                    getBatchRunWorkspace().refreshBatchRunResults();
                } else // batch run has no results, simply add the frapStudy into
                {
                    getBatchRunWorkspace().addFrapStudy(fStudy);
                }
                // set save flag true when a doc has been added successfully
                getBatchRunWorkspace().setSaveNeeded(true);
                // update tree
                DefaultMutableTreeNode newNode = frapBatchRunViewTree.addBatchRunDocNode(new File(getBatchRunWorkspace().getWorkingFrapStudy().getXmlFilename()));
                // get the new tree node after sorting
                newNode = frapBatchRunViewTree.orderFRAPDocChildren(newNode);
                frapBatchRunViewTree.setSelectionPath(new TreePath(newNode.getPath()));
            } else {
                // load data unsuccessfully, remove the displayed image
                getBatchRunWorkspace().clearWorkingSingleWorkspace();
                // clear tree selection
                frapBatchRunViewTree.clearSelection();
                // clear stored tree selection
                batchRunWorkspace.clearStoredTreeSelection();
            }
        }
    } else if (source == deleteButton) {
        AsynchClientTask deleteFromWorkspaceTask = new AsynchClientTask("deleting file ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                // remove tree node(doc node removable only)
                DefaultMutableTreeNode parent = frapBatchRunViewTree.removeCurrentNode();
                // handle differently for doc node and results node
                if (// doc node
                parent.equals(BatchRunTree.FRAP_BATCHRUN_DOC_NODE)) {
                    // remove the data & displayed image
                    getBatchRunWorkspace().removeFrapStudy(getBatchRunWorkspace().getWorkingFrapStudy());
                } else if (// results node
                parent.equals(BatchRunTree.FRAP_BATCHRUN_RESULT_NODE)) {
                    getBatchRunWorkspace().clearResultData();
                }
                getBatchRunWorkspace().clearWorkingSingleWorkspace();
            }
        };
        AsynchClientTask deleteFromUITask = new AsynchClientTask("deleting file ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                // clear tree selection
                frapBatchRunViewTree.clearSelection();
                if (batchRunWorkspace.getFrapStudies() == null || batchRunWorkspace.getFrapStudies().size() < 1) {
                    frapBatchRunViewTree.clearAll();
                } else // if doc has been deleted successfully and frapStudyList still has doc, set save flag true.
                {
                    batchRunWorkspace.setSaveNeeded(true);
                }
                batchRunWorkspace.clearStoredTreeSelection();
                // clear parameter display
                clearParameterDisplay();
            }
        };
        ClientTaskDispatcher.dispatch(BatchRunDetailsPanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { deleteFromWorkspaceTask, deleteFromUITask }, false, false, false, null, true);
    } else if (source == delAllButton) {
        deleteAllBatchrunDocs();
    }
}

Example 30 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class BatchRunResultsParamTablePanel method propertyChange.

public void propertyChange(PropertyChangeEvent evt) {
    if (evt.getPropertyName().equals(FRAPBatchRunWorkspace.PROPERTY_CHANGE_BATCHRUN_DETAILS)) {
        int rowNum = ((Integer) evt.getNewValue()).intValue();
        String fileName = ((File) table_param.getValueAt(rowNum, BatchRunResultsParamTableModel.COLUMN_FILE_NAME)).getAbsolutePath();
        // System.out.println("FileName---" + fileName);
        FRAPStudy selectedFrapStudy = batchRunWorkspace.getFRAPStudy(fileName);
        // display estimation result for each selected frapStudy based on model type
        if (batchRunWorkspace.getSelectedModel() == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT) {
            try {
                batchRunWorkspace.getWorkingSingleWorkspace().setFrapStudy(selectedFrapStudy, false, true);
                getOneDiffComponentPanel().setFrapWorkspace(batchRunWorkspace.getWorkingSingleWorkspace());
                getOneDiffComponentPanel().setData(selectedFrapStudy.getFrapOptData(), selectedFrapStudy.getFrapData(), selectedFrapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters(), selectedFrapStudy.getFrapData().getImageDataset().getImageTimeStamps(), selectedFrapStudy.getStartingIndexForRecovery(), selectedFrapStudy.getSelectedROIsForErrorCalculation());
            } catch (Exception e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
            int choice = DialogUtils.showComponentOKCancelDialog(JOptionPane.getFrameForComponent(BatchRunResultsParamTablePanel.this), getOneDiffComponentPanel(), "Estimation Details for " + selectedFrapStudy.getXmlFilename());
            if (choice == JOptionPane.OK_OPTION) {
                selectedFrapStudy.getFrapModel(FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT).setModelParameters(getOneDiffComponentPanel().getCurrentParameters());
                batchRunWorkspace.refreshStatisticsData();
            }
        } else if (batchRunWorkspace.getSelectedModel() == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS) {
            try {
                batchRunWorkspace.getWorkingSingleWorkspace().setFrapStudy(selectedFrapStudy, false, true);
                getTwoDiffComponentPanel().setFrapWorkspace(batchRunWorkspace.getWorkingSingleWorkspace());
                getTwoDiffComponentPanel().setData(selectedFrapStudy.getFrapOptData(), selectedFrapStudy.getFrapData(), selectedFrapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters(), selectedFrapStudy.getFrapData().getImageDataset().getImageTimeStamps(), selectedFrapStudy.getStartingIndexForRecovery(), selectedFrapStudy.getSelectedROIsForErrorCalculation());
            } catch (Exception e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
            int choice = DialogUtils.showComponentOKCancelDialog(JOptionPane.getFrameForComponent(BatchRunResultsParamTablePanel.this), getTwoDiffComponentPanel(), "Estimation Details for " + selectedFrapStudy.getXmlFilename());
            if (choice == JOptionPane.OK_OPTION) {
                selectedFrapStudy.getFrapModel(FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS).setModelParameters(getTwoDiffComponentPanel().getCurrentParameters());
                batchRunWorkspace.refreshStatisticsData();
            }
        } else if (batchRunWorkspace.getSelectedModel() == FRAPModel.IDX_MODEL_REACTION_OFF_RATE) {
            try {
                batchRunWorkspace.getWorkingSingleWorkspace().setFrapStudy(selectedFrapStudy, false, true);
                getOffRatePanel().setFrapWorkspace(batchRunWorkspace.getWorkingSingleWorkspace());
                getOffRatePanel().setData(selectedFrapStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters(), selectedFrapStudy.getFrapData(), selectedFrapStudy.getStartingIndexForRecovery());
            } catch (Exception e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
            int choice = DialogUtils.showComponentOKCancelDialog(JOptionPane.getFrameForComponent(BatchRunResultsParamTablePanel.this), getOffRatePanel(), "Estimation Details for " + selectedFrapStudy.getXmlFilename());
            if (choice == JOptionPane.OK_OPTION) {
                selectedFrapStudy.getFrapModel(FRAPModel.IDX_MODEL_REACTION_OFF_RATE).setModelParameters(getOffRatePanel().getCurrentParameters());
                batchRunWorkspace.refreshStatisticsData();
            }
        }
    }
}