enh: add developer mode for loading creep-compliance data (close #14)

AFM-analysis · Jul 9, 2021 · 504c7f6 · 504c7f6
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commit 504c7f6
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Showing 4 changed files with 54 additions and 3 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,5 +1,6 @@
 0.9.2
  - ref: improve speed when displaying QMap data
+ - enh: add developer mode for loading creep-compliance data (#14)
  - setup: bump afmformats from 0.13.3 to 0.14.3 (mostly speed,
    support AFM workshop maps)
  - setup: bump nanite from 1.7.4 to 1.7.6 (mostly speed)

diff --git a/docs/sec_interface.rst b/docs/sec_interface.rst
@@ -244,3 +244,15 @@ documentation <nanite:sec_rating>`.
 The button at the bottom starts the PyJibe curve rater which is compatible
 to the nanite rating workflow. If you would like to import your own training
 set, please read the quick guide :ref:`sec_qg_import_ts`.
+
+
+Developer mode
+==============
+Under *Edit | Developer mode*, you can enable developer mode which will:
+
+- Allow you to open experimental data that were not recorded via
+  force-distance modality (e.g. creep-compliance). Related issues are
+  `nanite #11 <https://github.com/AFM-analysis/nanite/issues/11>`_ and
+  `afmformats #15 <https://github.com/AFM-analysis/afmformats/issues/15>`_.
+- Slow down loading of large datasets (because the modality has to be
+  determined first).
diff --git a/pyjibe/head/main.py b/pyjibe/head/main.py
@@ -15,6 +15,7 @@
 import h5py
 import lmfit
 import nanite
+import nanite.read
 import numpy
 import scipy
 import sklearn
@@ -67,6 +68,11 @@ def __init__(self, *args, **kwargs):
         self.action_open_bulk.triggered.connect(self.on_open_bulk)
         self.action_open_single.triggered.connect(self.on_open_single)
         self.action_open_multiple.triggered.connect(self.on_open_multiple)
+        # Edit menu
+        is_dev_mode = bool(int(self.settings.value("developer mode", "0")))
+        self.action_developer_mode.setChecked(is_dev_mode)
+        self.on_developer_mode(is_dev_mode)
+        self.action_developer_mode.triggered.connect(self.on_developer_mode)
         # Tool menu
         self.actionConvert_AFM_data.triggered.connect(self.on_tool_convert)
         # Help menu
@@ -146,6 +152,7 @@ def rem_subwindow(self, title):
                 self.menuExport.removeAction(action)
                 break
 
+    @QtCore.pyqtSlot()
     def on_about(self):
         about_text = "PyJibe is a user interface for data analysis in " \
             + "atomic force microscopy with an emphasis on biological " \
@@ -157,10 +164,22 @@ def on_about(self):
                                     "PyJibe {}".format(__version__),
                                     about_text)
 
+    @QtCore.pyqtSlot(bool)
+    def on_developer_mode(self, checked):
+        # remember in settings
+        self.settings.setValue("developer mode", str(int(checked)))
+        # set nanite
+        if checked:
+            nanite.read.DEFAULT_MODALITY = None
+        else:
+            nanite.read.DEFAULT_MODALITY = "force-distance"
+
+    @QtCore.pyqtSlot()
     def on_documentation(self):
         webbrowser.open("https://pyjibe.readthedocs.io")
 
-    def on_open_bulk(self, evt=None):
+    @QtCore.pyqtSlot()
+    def on_open_bulk(self):
         dlg = custom_widgets.DirectoryDialogMultiSelect(self)
         search_dir = self.settings.value("paths/load data", "")
         dlg.setDirectory(search_dir)
@@ -172,7 +191,8 @@ def on_open_bulk(self, evt=None):
                 self.settings.setValue("paths/load data",
                                        str(dlg.getDirectory()))
 
-    def on_open_multiple(self, evt=None):
+    @QtCore.pyqtSlot()
+    def on_open_multiple(self):
         dlg = custom_widgets.DirectoryDialogMultiSelect(self)
         search_dir = self.settings.value("paths/load data", "")
         dlg.setDirectory(search_dir)
@@ -185,7 +205,8 @@ def on_open_multiple(self, evt=None):
                 self.settings.setValue("paths/load data",
                                        str(dlg.getDirectory()))
 
-    def on_open_single(self, evt=None):
+    @QtCore.pyqtSlot()
+    def on_open_single(self):
         ext_opts = []
         # all
         exts = ["*"+e for e in registry.known_suffixes]
@@ -206,6 +227,7 @@ def on_open_single(self, evt=None):
             self.settings.setValue("paths/load data",
                                    str(pathlib.Path(n[0]).parent))
 
+    @QtCore.pyqtSlot()
     def on_software(self):
         libs = [afmformats,
                 h5py,
@@ -228,6 +250,7 @@ def on_software(self):
                                           "Software",
                                           sw_text)
 
+    @QtCore.pyqtSlot()
     def on_tool_convert(self):
         dlg = ConvertDialog(self)
         dlg.show()

diff --git a/pyjibe/head/main.ui b/pyjibe/head/main.ui
@@ -109,7 +109,14 @@
     </property>
     <addaction name="actionConvert_AFM_data"/>
    </widget>
+   <widget class="QMenu" name="menuPreferences">
+    <property name="title">
+     <string>&amp;Edit</string>
+    </property>
+    <addaction name="action_developer_mode"/>
+   </widget>
    <addaction name="menu_File"/>
+   <addaction name="menuPreferences"/>
    <addaction name="menuExport"/>
    <addaction name="menuTools"/>
    <addaction name="menuHelp"/>
@@ -174,6 +181,14 @@
     <string>Convert AFM data</string>
    </property>
   </action>
+  <action name="action_developer_mode">
+   <property name="checkable">
+    <bool>true</bool>
+   </property>
+   <property name="text">
+    <string>&amp;Developer mode</string>
+   </property>
+  </action>
  </widget>
  <resources/>
  <connections/>