Merge pull request #18 from djdt/laser_sync

ESL laser log importer

docs/dialogs/import.rst

@@ -82,6 +82,47 @@ Parameters from :ref:`laser_parameters` will be automatically read from imports
    | Scantime  | s    | Acquistion time for each pixel; Total dwell time for all elements. |
    +----------+-------+--------------------------------------------------------------------+
 
+
+LaserLog Import Wizard
+-----------------------
+.. index:: LaserLog Import Wizard
+
+* **File -> Import -> ESL Laser Log Wizard**
+* **Drag-and-Drop -> Log and laser data files**
+
+This wizard guides you through importing ICP-MS data and aligning it with a ESL laser ablation log file.
+ICP-MS data should be collected as one line/sample or one file per laser pattern, multiple batches can be imported per log.
+
+.. note::
+    To use this import make sure to activate the **save Iolite log file** option on the ActiveView2 home page, *before ablating*. 
+
+On the first page open or drag-and-drop the laser log file, this is usually named in the format 'LaserLog_YY-mm-dd_HH-MM-SS.csv'.
+
+The next two pages import laser data and instructions in `Import Wizard` should be followed.
+Only data formats that save the event times are supported (Agilent batches, Perkin-Elmer 'XL' and Thermo iCap CSV).
+
+.. warning:: 
+    Currently only Agilent data has been tested with the importer.
+
+.. figure:: ../images/dialog_nwi_import.png
+    :width: 480px
+    :align: center
+    :name: nwi_laser_group
+
+    The ESL Import groups page. Here both pattern per sample and pattern per file data has been selected for import.
+
+The groups page shows all imported patterns and data files.
+Drag the laser files to match with their corresponding laser log patterns.
+
+Checking the *Split data into rows* can be used if data has been collected as one line/sample per pattern.
+This will add a *row X* parameter to each laser line, as in :ref:`nwi_laser_group`.
+
+Imported data is previewed on the next page, and the back button can be used to make changes to pattern-laser groupings.
+A *Delay* control is provided for instrument setups with a long transport time (time taken for ablations to reach the ICP-MS).
+Laser images are imported with their real world positions and parameters and a final control,
+*Remove space between images*, can be used to collapse any empty space between images and make the scene more compact.
+
+
 Spot-wise Import Wizard
 -----------------------
 .. index:: Spot-wise Import Wizard
@@ -176,16 +217,16 @@ The `Difference` output will show the difference in the shape to the current pea
 Rastered collections should enabled the alternating raster option.
 Once the image is correct the spotsize can be entered on the following page.
 
-Kriss-Kross Import Wizard
--------------------------
-.. index:: Kriss-Kross Import Wizard
-
-* **File -> Import -> Kriss-Kross Import Wizard**
-
-Import of Kriss-Kross_ collected Super-Resolution-Reconstruction images is performed
-using the `Kriss-Kross Import Wizard`. This will guide users through import of the data
-in a simliar manner to the :ref:`Import Wizard`.
-
-.. seealso::
-    :ref:`Example: Importing file-per-line data`.
-     Example showing how to use the import wizard.
+.. Kriss-Kross Import Wizard
+.. -------------------------
+.. .. index:: Kriss-Kross Import Wizard
+..
+.. * **File -> Import -> Kriss-Kross Import Wizard**
+..
+.. Import of Kriss-Kross_ collected Super-Resolution-Reconstruction images is performed
+.. using the `Kriss-Kross Import Wizard`. This will guide users through import of the data
+.. in a simliar manner to the :ref:`Import Wizard`.
+..
+.. .. seealso::
+..     :ref:`Example: Importing file-per-line data`.
+..      Example showing how to use the import wizard.

pewpew/graphics/lasergraphicsview.py

@@ -1,4 +1,3 @@
-
 import numpy as np
 from pewlib.process.register import fft_register_offset
 from PySide6 import QtCore, QtGui, QtWidgets
@@ -24,14 +23,22 @@
 )
 
 
+class IgnoreRightButtonScene(QtWidgets.QGraphicsScene):
+    def mousePressEvent(self, event: QtGui.QMouseEvent):
+        if event.button() == QtCore.Qt.MouseButton.RightButton:
+            event.accept()
+        else:
+            super().mousePressEvent(event)
+
+
 class LaserGraphicsView(OverlayGraphicsView):
     """The pewpew laser view."""
 
     def __init__(
         self, options: GraphicsOptions, parent: QtWidgets.QWidget | None = None
     ):
         super().__init__(
-            QtWidgets.QGraphicsScene(QtCore.QRectF(-1e5, -1e5, 2e5, 2e5), parent),
+            IgnoreRightButtonScene(QtCore.QRectF(-1e5, -1e5, 2e5, 2e5), parent),
             parent,
         )
         self.setDragMode(QtWidgets.QGraphicsView.DragMode.RubberBandDrag)
@@ -51,15 +58,6 @@ def __init__(
         self.options.visiblityOptionsChanged.connect(self.updateOverlayVisibility)
         self.viewScaleChanged.connect(self.scalebar.requestPaint)
 
-        # self.shown = False
-
-    # def showEvent(self, event: QtGui.QShowEvent) -> None:
-    # super().showEvent(event)
-    # if not self.shown:
-    #     print('shown')
-    #     self.zoomReset()
-    #     self.shown = True
-
     def laserItems(self) -> list[LaserImageItem]:
         return [
             item
@@ -69,8 +67,18 @@ def laserItems(self) -> list[LaserImageItem]:
             if isinstance(item, LaserImageItem)
         ]
 
+    def selectedLaserItems(self) -> list[LaserImageItem]:
+        return [
+            item
+            for item in self.scene().selectedItems()
+            if isinstance(item, LaserImageItem)
+        ]
+
     def alignLaserItemsFFT(self) -> None:
-        items = self.laserItems()
+        items = self.selectedLaserItems()
+        if len(items) == 0:
+            items = self.laserItems()
+
         base = items[0]
         for item in items[1:]:
             offset = fft_register_offset(base.rawData(), item.rawData())
@@ -79,25 +87,28 @@ def alignLaserItemsFFT(self) -> None:
                 base.pos()
                 + QtCore.QPointF(offset[1] * psize.width(), offset[0] * psize.height())
             )
-        self.zoomReset()
 
     def alignLaserItemsLeftToRight(self) -> None:
-        items = self.laserItems()
+        items = self.selectedLaserItems()
+        if len(items) == 0:
+            items = self.laserItems()
+
         base = items[0]
         pos = base.pos() + QtCore.QPointF(base.boundingRect().width(), 0.0)
         for item in items[1:]:
             item.setPos(pos)
             pos.setX(pos.x() + item.boundingRect().width())
-        self.zoomReset()
 
     def alignLaserItemsTopToBottom(self) -> None:
-        items = self.laserItems()
+        items = self.selectedLaserItems()
+        if len(items) == 0:
+            items = self.laserItems()
+
         base = items[0]
         pos = base.pos() + QtCore.QPointF(0.0, base.boundingRect().height())
         for item in items[1:]:
             item.setPos(pos)
             pos.setY(pos.y() + item.boundingRect().height())
-        self.zoomReset()
 
     def focusOutEvent(self, event: QtGui.QFocusEvent) -> None:
         self.clearFocus()

pewpew/graphics/options.py

@@ -7,7 +7,6 @@ class GraphicsOptions(QtCore.QObject):
     """This object stores information used by pewpew to draw images.
 
     Parameters:
-        items: dict of item visibilities
         colortable: colortable to draw with, see colortables
         colorrange_default: default colorrange to use
         smoothing: whether to smooth images

pewpew/mainwindow.py

@@ -4,6 +4,7 @@
 from types import TracebackType
 
 from pewlib.config import Config, SpotConfig
+from pewlib.io.laser import is_nwi_laser_log
 from PySide6 import QtCore, QtGui, QtWidgets
 
 from pewpew.actions import qAction, qActionGroup
@@ -12,7 +13,7 @@
 from pewpew.widgets import dialogs
 from pewpew.widgets.exportdialogs import ExportAllDialog
 from pewpew.widgets.laser import LaserTabView
-from pewpew.widgets.wizards import ImportWizard, SpotImportWizard
+from pewpew.widgets.wizards import ImportWizard, LaserLogImportWizard, SpotImportWizard
 
 logger = logging.getLogger(__name__)
 
@@ -27,6 +28,8 @@ def __init__(self, parent: QtWidgets.QWidget | None = None):
         super().__init__(parent)
         self.resize(1280, 800)
 
+        self.setAcceptDrops(True)
+
         self.log = LoggingDialog()
         self.help = HelpDialog()
 
@@ -54,6 +57,38 @@ def __init__(self, parent: QtWidgets.QWidget | None = None):
 
         self.default_config = Config()
 
+    def dragEnterEvent(self, event: QtGui.QDragEnterEvent) -> None:
+        if event.mimeData().hasUrls():
+            paths = [Path(url.toLocalFile()) for url in event.mimeData().urls()]
+            if any(is_nwi_laser_log(path) for path in paths):
+                event.acceptProposedAction()
+        super().dragEnterEvent(event)
+
+    def dropEvent(self, event: QtGui.QDropEvent) -> None:
+        if not event.mimeData().hasUrls():
+            return super().dropEvent(event)
+        log_paths = []
+        paths = []
+        for url in event.mimeData().urls():
+            path = Path(url.toLocalFile())
+            if is_nwi_laser_log(path):
+                log_paths.append(path)
+            else:
+                paths.append(path)
+
+        wiz = LaserLogImportWizard(
+            path=log_paths[0],
+            laser_paths=paths,
+            options=self.tabview.options,
+            parent=self,
+        )
+        wiz.laserImported.connect(self.tabview.importFile)
+        wiz.laserImported.connect(
+            lambda: self.tabview.activeWidget().graphics.zoomReset()
+        )
+        wiz.open()
+        event.acceptProposedAction()
+
     def createActions(self) -> None:
         self.action_about = qAction(
             "help-about", "&About", "About pew².", self.actionAbout
@@ -182,9 +217,15 @@ def createActions(self) -> None:
         self.action_wizard_import = qAction(
             "",
             "Import Wizard",
-            "Start the line-wise import wizard. .",
+            "Start the line-wise import wizard.",
             self.actionWizardImport,
         )
+        self.action_wizard_laserlog = qAction(
+            "",
+            "ESL Laser Log Wizard",
+            "Import data and sync to a ESL ActiveView2 log file.",
+            self.actionWizardLaserLog,
+        )
         self.action_wizard_spot = qAction(
             "",
             "Spotwise Wizard",
@@ -210,6 +251,7 @@ def createMenus(self) -> None:
         # File -> Import
         menu_import = menu_file.addMenu("&Import")
         menu_import.addAction(self.action_wizard_import)
+        menu_import.addAction(self.action_wizard_laserlog)
         menu_import.addAction(self.action_wizard_spot)
         # menu_import.addAction(self.action_wizard_srr)
 
@@ -402,6 +444,15 @@ def actionWizardSpot(self) -> QtWidgets.QWizard:
         wiz.open()
         return wiz
 
+    def actionWizardLaserLog(self) -> QtWidgets.QWizard:
+        wiz = LaserLogImportWizard(options=self.tabview.options, parent=self)
+        wiz.laserImported.connect(self.tabview.importFile)
+        wiz.laserImported.connect(
+            lambda: self.tabview.activeWidget().graphics.zoomReset()
+        )
+        wiz.open()
+        return wiz
+
     # def actionWizardSRR(self) -> QtWidgets.QWizard:
     #     wiz = SRRImportWizard(config=self.tabview.config, parent=self)
     #     wiz.laserImported.connect(self.tabview.importFile)