Merge pull request #290 from NaturalHistoryMuseum/feature/212-box-order

[#212] loads of work on box sorting

.travis.yml

@@ -8,11 +8,28 @@ virtualenv:
 
 before_install:
   - sudo apt-get update
-
-install:
   - if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then
-      sudo apt-get install --fix-missing python-opencv python-numpy python-pyside libtiff4-dev libjpeg8-dev zlib1g-dev libzbar-dev;
+      sudo apt-get install -y --fix-missing libzbar-dev;
+    fi
+
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
     fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update --yes conda
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION pillow pyside numpy scikit-learn opencv
+  - source activate test-environment
+  - python setup.py install
+
+install:
   - pip install -r requirements.txt
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"

CHANGELOG.md

@@ -2,10 +2,12 @@ This is an overview of major changes. Refer to the git repository for a full log
 
 Version 0.1.28
 -------------
+- Fixed #291 - Alter travis to use Anaconda / Miniconda
 - Fixed #288 - Minimap navigator
 - Fixed #286 - Disable default template command when the default template selected
 - Fixed #284 - Document info view to contain links
 - Fixed #281 - Don't make images read-only
+- Fixed #212 - Customized bounding box ordering
 - Fixed #204 - Improvements to subsegment dots
 - Fixed #203 - Resize handles should have constant size regardless of zoom
 

DevelopingOnMacOSX.md

@@ -35,19 +35,24 @@ cd ~/projects/inselect
 pip install -r requirements.txt
 ```
 
-# OpenCV
-`numpy` is pinned by opencv installation
+## OpenCV
+Version of `numpy` is pinned by opencv installation but we want latest version -
+I have not encountered any problems by installing the latest version.
 
+`jjhelmus` provides versions after `2.4.10` but these make the Mac build
+extremely problematic by introducing many `dylib` dependencies that are
+troublesome to freeze.
 ```
-conda install --yes -c https://conda.binstar.org/jjhelmus opencv
+conda install --yes -c https://conda.binstar.org/jjhelmus opencv=2.4.10
+conda install --yes numpy
 ```
 
-# setuptools
+## setuptools
 A [bug in PyInstaller 3.1.1](https://github.com/pyinstaller/pyinstaller/issues/1773)
 means that we need to use setupools 19.2:
 
 ```
-conda install setuptools=19.2
+conda install --yes setuptools=19.2
 ```
 
 ## LibDMTX barcode reading library

DevelopingOnWindows.md

@@ -25,7 +25,7 @@ follows:
 
 ```
 conda update --yes conda
-conda create --yes --name inselect pillow pyside pywin32 numpy
+conda create --yes --name inselect pillow pyside pywin32 numpy scikit-learn
 activate inselect
 python -m pip install --upgrade pip
 pip install -r requirements.txt
@@ -92,7 +92,7 @@ follows:
 
 ```
 conda update --yes conda
-conda create --yes --name inselect pillow pyside pywin32 numpy
+conda create --yes --name inselect pillow pyside pywin32 numpy scikit-learn
 activate inselect
 python -m pip install --upgrade pip
 pip install -r requirements.txt

build.sh

@@ -24,10 +24,14 @@ if [[ "$OSTYPE" == "darwin"* ]]; then
     rm -rf build dist
     pyinstaller --clean inselect.spec
 
-    for script in export_metadata ingest read_barcodes save_crops segment; do
+    for script in export_metadata ingest read_barcodes save_crops; do
         rm -rf $script.spec
-        pyinstaller --onefile --icon=data/inselect.icns inselect/scripts/$script.py
+        pyinstaller --onefile --hidden-import numpy inselect/scripts/$script.py
     done
+    # segment has an additional hidden import
+    rm -rf segment.spec
+    pyinstaller --onefile --hidden-import numpy \
+        --hidden-import sklearn.neighbors.typedefs inselect/scripts/segment.py
 
     # Add a few items to the PropertyList file generated by PyInstaller
     python -m bin.plist dist/inselect.app/Contents/Info.plist

inselect.spec

@@ -1,6 +1,7 @@
 # For PyInstaller build on Mac
 
 import sys
+
 from pathlib import Path
 
 block_cipher = None
@@ -9,7 +10,7 @@ a = Analysis(['inselect.py'],
              pathex=[str(Path('.').absolute())],
              binaries=None,
              datas=None,
-             hiddenimports=[],
+             hiddenimports=['sklearn.neighbors.typedefs'],
              hookspath=[],
              runtime_hooks=[],
              excludes=['Tkinter'],
@@ -18,23 +19,25 @@ a = Analysis(['inselect.py'],
              cipher=block_cipher)
 
 
-# PyInstaller does not detect some dylibs, I think because they are symlinked.
+# PyInstaller does not detect some dylibs, I think in some cases because they
+# are symlinked.
 # See Stack Overflow post http://stackoverflow.com/a/17595149 for example
 # of manipulating Analysis.binaries.
 
-# Tuples (name, source)
 MISSING_DYLIBS = (
-    ('libQtCore.4.dylib', 'libQtCore.4.8.7.dylib'),
-    ('libQtGui.4.dylib', 'libQtGui.4.8.7.dylib'),
-    ('libpng16.16.dylib', 'libpng16.16.dylib'),
-    ('libz.1.dylib', 'libz.1.dylib'),
+    'libQtCore.4.dylib',
+    'libQtGui.4.dylib',
+    'libpng16.16.dylib',
+    'libz.1.dylib',
 )
 
 # The lib directory associated with this environment
 LIB = Path(sys.argv[0]).parent.parent.joinpath('lib')
 
-a.binaries += TOC([(name, str(LIB.joinpath(source)), 'BINARY') for name, source in MISSING_DYLIBS])
-
+# Find the source for each library and add it to the list of binaries
+a.binaries += TOC([
+    (lib, str(LIB.joinpath(lib).resolve()), 'BINARY') for lib in MISSING_DYLIBS
+])
 pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher)
 
 # Prefer to freeze to a folder rather than a single file. The choice makes no
@@ -51,7 +54,7 @@ if SINGLE_FILE:
               name='inselect',
               debug=False,
               strip=False,
-              upx=True,
+              upx=False,
               console=False,
               icon='data/inselect.icns')
 else:
@@ -62,7 +65,7 @@ else:
               name='inselect',
               debug=False,
               strip=False,
-              upx=True,
+              upx=False,
               console=False,
               icon='data/inselect.icns')
 
@@ -71,7 +74,7 @@ else:
                    a.zipfiles,
                    a.datas,
                    strip=False,
-                   upx=True,
+                   upx=False,
                    name='inselect')
 
 

inselect/gui/main_window.py

@@ -32,6 +32,7 @@
 from .plugins.subsegment import SubsegmentPlugin
 from .recent_documents import RecentDocuments
 from .roles import RotationRole
+from .sort_document_items import sort_items_choice
 from .user_template_choice import user_template_choice
 from .utils import contiguous, report_to_user, qimage_of_bgr
 from .views.boxes import BoxesView, GraphicsItemView
@@ -963,11 +964,11 @@ def _create_menu_actions(self):
             triggered=partial(self.select_next_prev, next=False)
         )
         self.select_by_size_larger_action = QAction(
-            "Select increasing size", self, shortcut="ctrl+>",
+            "Select &increasing size", self, shortcut="ctrl+>",
             triggered=partial(self.select_by_size_step, larger=True)
         )
         self.select_by_size_smaller_action = QAction(
-            "Select decreasing size", self, shortcut="ctrl+<",
+            "Select d&ecreasing size", self, shortcut="ctrl+<",
             triggered=partial(self.select_by_size_step, larger=False)
         )
 
@@ -984,14 +985,23 @@ def _create_menu_actions(self):
                                              self.delete_action.shortcut()])
 
         self.rotate_clockwise_action = QAction(
-            "Rotate clockwise", self, shortcut="ctrl+R",
+            "Rotate c&lockwise", self, shortcut="ctrl+R",
             triggered=partial(self.rotate90, clockwise=True)
         )
         self.rotate_counter_clockwise_action = QAction(
-            "Rotate counter-clockwise", self, shortcut="ctrl+L",
+            "Rotate c&ounter-clockwise", self, shortcut="ctrl+L",
             triggered=partial(self.rotate90, clockwise=False)
         )
 
+        self.sort_by_rows_action = QAction(
+            "Sort by &rows", self, checkable=True,
+            triggered=partial(self.sort_boxes, by_columns=False)
+        )
+        self.sort_by_columns_action = QAction(
+            "Sort by &columns", self, checkable=True,
+            triggered=partial(self.sort_boxes, by_columns=True)
+        )
+
         # Plugins
         # Plugin shortcuts start at F5
         shortcut_offset = 5
@@ -1054,7 +1064,7 @@ def _create_menu_actions(self):
             icon=self.style().standardIcon(QtGui.QStyle.SP_ArrowDown)
         )
         self.zoom_home_action = QAction(
-            "Whole image", self,
+            "&Whole image", self,
             shortcut=QtGui.QKeySequence.MoveToStartOfDocument,
             triggered=self.zoom_home, checkable=True
         )
@@ -1071,10 +1081,10 @@ def _create_menu_actions(self):
         )
 
         self.show_object_grid_action = QAction(
-            'Show grid', self, shortcut='ctrl+G', triggered=self.show_grid
+            'Show &grid', self, shortcut='ctrl+G', triggered=self.show_grid
         )
         self.show_object_expanded_action = QAction(
-            'Show expanded', self,
+            'Show &expanded', self,
             shortcut='ctrl+E', triggered=self.show_expanded
         )
 
@@ -1184,6 +1194,9 @@ def _create_menus(self):
         self._edit_menu.addAction(self.rotate_clockwise_action)
         self._edit_menu.addAction(self.rotate_counter_clockwise_action)
         self._edit_menu.addSeparator()
+        self._edit_menu.addAction(self.sort_by_rows_action)
+        self._edit_menu.addAction(self.sort_by_columns_action)
+        self._edit_menu.addSeparator()
         user_template_popup = self._edit_menu.addMenu('Metadata template')
         self.view_metadata.popup_button.inject_actions(user_template_popup)
         self._edit_menu.addSeparator()
@@ -1210,7 +1223,7 @@ def _create_menus(self):
         self._view_menu.addAction(self.show_object_grid_action)
         self._view_menu.addAction(self.show_object_expanded_action)
         self._view_menu.addSeparator()
-        colours_popup = self._view_menu.addMenu('Colour scheme')
+        colours_popup = self._view_menu.addMenu('&Colour scheme')
         for action in self.colour_scheme_actions:
             colours_popup.addAction(action)
 
@@ -1345,6 +1358,22 @@ def copy_to_new_document(self):
             else:
                 self.new_document(path, default_metadata_items=items)
 
+    @report_to_user
+    def sort_boxes(self, by_columns):
+        """Sorts boxes either by columns or by rows.
+        """
+        if self.document:
+            # Sort boxes
+            self.model.to_document(self.document)
+            items = sort_items_choice().sort_items(
+                self.document.items, by_columns
+            )
+            self.model.set_new_boxes(items)
+        else:
+            # Record the user's choice
+            sort_items_choice().sort_items([], by_columns)
+        self.sync_ui()
+
     def _accept_drag_drop(self, event):
         """If event refers to a single file that can opened, returns the path.
         Returns None otherwise.
@@ -1428,6 +1457,8 @@ def sync_ui(self):
         self.delete_action.setEnabled(has_selection)
         self.rotate_clockwise_action.setEnabled(has_selection)
         self.rotate_counter_clockwise_action.setEnabled(has_selection)
+        self.sort_by_rows_action.setChecked(not sort_items_choice().by_columns)
+        self.sort_by_columns_action.setChecked(sort_items_choice().by_columns)
         self.cookie_cutter_widget.sync_actions(document, has_rows)
         for action in self.plugin_actions:
             action.setEnabled(document)

inselect/gui/plugins/segment.py

@@ -1,8 +1,10 @@
 from PySide.QtGui import QIcon, QMessageBox
 
-from inselect.lib.segment import segment_document
+from inselect.lib.segment_document import SegmentDocument
 from inselect.lib.utils import debug_print
 
+from inselect.gui.sort_document_items import sort_items_choice
+
 from .plugin import Plugin
 
 
@@ -16,6 +18,7 @@ def __init__(self, document, parent):
         self.rects = self.display = None
         self.document = document
         self.parent = parent
+        self.sort_choice = sort_items_choice().by_columns
 
     @classmethod
     def icon(cls):
@@ -34,8 +37,12 @@ def can_be_run(self):
 
     def __call__(self, progress):
         debug_print('SegmentPlugin.__call__')
-        doc, display = segment_document(self.document, callback=progress)
+        doc, display = SegmentDocument(self.sort_choice).segment(
+            self.document, callback=progress
+        )
 
         self.items, self.display = doc.items, display
 
-        debug_print('SegmentPlugin.__call__ exiting. Found [{0}] boxes'.format(len(self.items)))
+        debug_print('SegmentPlugin.__call__ exiting. Found [{0}] boxes'.format(
+            len(self.items))
+        )