- fix: missing title in FD window and missing FD number in export menu

 - docs: add quick guide for importing a nanite training set
 - docs: add black/white logo

CHANGELOG

@@ -1,3 +1,7 @@
+0.5.1
+ - fix: missing title in FD window and missing FD number in export menu
+ - docs: add quick guide for importing a nanite training set
+ - docs: add black/white logo
 0.5.0
  - feat: allow to import training sets produced with nanite
  - ref: major code refactoring of force-distance interface and cleanup

docs/index.rst

@@ -1,7 +1,7 @@
 .. _index:
 
 
-.. image:: logo/PyJibe.png
+.. image:: logo/PyJibe_bw.png
 
 |
 
@@ -19,6 +19,7 @@ Documentation
    :maxdepth: 2
 
    sec_getting_started
+   sec_quick_guides
 
 .. toctree::
    :maxdepth: 1

docs/pyjibe.bib

@@ -1,3 +1,10 @@
 % Encoding: UTF-8
 
-
+@Article{zef18,
+  author  = {Paul Müller and Stephanie Möllmert and Jochen Guck},
+  title   = {{Atomic force microscopy indentation data of zebrafish spinal cord sections}},
+  journal = {Figshare},
+  year    = {2018},
+  month   = {11},
+  doi     = {10.6084/m9.figshare.7297202.v1},
+}

docs/sec_qg_import_ts.rst

@@ -0,0 +1,32 @@
+.. _sec_qg_import_ts:
+
+=====================================
+Importing a pre-computed training set
+=====================================
+
+A training set is a set of text files containing rating features
+and manual user ratings. Training sets are the basis of the rating
+scheme employed in PyJibe (and nanite). By default, PyJibe
+comes with the *zef18* training set :cite:`zef18`. For general information
+about how manual rating and generation of the training set works, please
+refer to the :ref:`nanite rating workflow <nanite:sec_rating>`.
+
+In order to import a training set into PyJibe,
+the text files (``train_feat_*.txt`` and ``train_response.txt``) must be
+zipped and named according to the scheme
+``ts_NAME.zip``, where ``NAME`` is a descriptive name. 
+
+.. image:: scrots/qg_import_ts.png
+    :target: _images/qg_import_ts.png
+    :align: right
+    :scale: 100%
+
+The import in PyJibe is carried out by selecting *Add...* in the
+*Scheme* dropdown menu, located in the *Curve rating* box
+(lower right of a Force-Distance analysis).
+A dialog will ask for the zipped training set (e.g. ``ts_organoids19.zip``). 
+
+The import is persistent, i.e. the training set is extracted to the
+user's configuration directory and thus does not have to be imported
+again the next time PyJibe is run. 
+

docs/sec_quick_guides.rst

@@ -0,0 +1,9 @@
+============
+Quick Guides
+============
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   sec_qg_import_ts

pyjibe/fd/main.py

@@ -33,8 +33,7 @@ def __init__(self, *args, **kwargs):
         uic.loadUi(path_ui, self)
 
         UiForceDistance._instance_counter += 1
-        title = "{} #{}".format(self.parent().windowTitle(),
-                                self._instance_counter)
+        title = "Force-Distance #{}".format(self._instance_counter)
         self.parent().setWindowTitle(title)
 
         self.data_set = nanite.IndentationGroup()
@@ -522,7 +521,7 @@ def rating_scheme_setup(self):
         self.cb_rating_scheme.clear()
         schemes = rating_base.get_rating_schemes()
         self.cb_rating_scheme.addItems(list(schemes.keys()))
-        self.cb_rating_scheme.addItem("Import...")
+        self.cb_rating_scheme.addItem("Add...")
 
 
 class AbortProgress(BaseException):

pyjibe/head/main.py

@@ -57,7 +57,7 @@ def add_subwindow(self, aclass, flist):
         # Add export choices
         if hasattr(inst, "get_export_choices"):
             choices = inst.get_export_choices()
-            menobj = self.menuExport.addMenu(inst.windowTitle())
+            menobj = self.menuExport.addMenu(sub.windowTitle())
             for choice in choices:
                 action = menobj.addAction(choice[0])
                 action.triggered.connect(getattr(inst, choice[1]))