fix: minor visualization issues

AFM-analysis · Nov 16, 2020 · 96b4ac7 · 96b4ac7
1 parent 12eba53
commit 96b4ac7
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Showing 17 changed files with 16 additions and 9 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -2,7 +2,11 @@
  - fix: main window not focused after startup
  - fix: Windows installation location was confusing and did
    not coincide configuration file location
- - setup: bump afmformats from 0.11.0 to 0.12.0
+ - fix: files are sorted before batch loading
+ - fix: change visualization of fitting region by gray
+   wraparound instead of yellow highlight (not visible
+   on all screens)
+ - setup: bump afmformats from 0.11.0 to 0.12.2
    (improved JPK file format speed)
 0.8.2
  - setup: bump matplotlib to >=3

diff --git a/docs/scrots/.gitignore b/docs/scrots/.gitignore
@@ -1,4 +1,5 @@
 _*.png
+*.jpk-force
 *.jpk-force-map
 *.tsv
 figshare_PAAm
diff --git a/docs/scrots/make_scrots_qg_import_ts.py b/docs/scrots/make_scrots_qg_import_ts.py
@@ -1,12 +1,13 @@
 """Screenshots for quick guide import ts (not working automatically)"""
 import pathlib
 import sys
+import time
 
 from PyQt5 import QtCore
 from PyQt5.QtWidgets import QApplication
 from pyjibe.head.main import PyJibe
 
-jpkfile = pathlib.Path("figshare_PAAm/PAAm_Compliant_ROI1_force-save-"
+jpkfile = pathlib.Path("PAAm_Compliant_ROI1_force-save-"
                        + "2019.10.25-10.42.02.660.jpk-force")
 
 
@@ -37,7 +38,6 @@ def cleanup_autosave(jpkfile):
 war.grab().save("_qg_import_ts.png")
 
 print("Screenshot must be taken manually")
-import IPython  # noqa: E402
-IPython.embed()
+time.sleep(10)
 
 mw.close()
diff --git a/docs/scrots/ui_fd_main.png b/docs/scrots/ui_fd_main.png
diff --git a/docs/scrots/ui_fd_tab_edelta.png b/docs/scrots/ui_fd_tab_edelta.png
diff --git a/docs/scrots/ui_fd_tab_fit.png b/docs/scrots/ui_fd_tab_fit.png
diff --git a/docs/scrots/ui_fd_tab_info.png b/docs/scrots/ui_fd_tab_info.png
diff --git a/docs/scrots/ui_fd_tab_preproc.png b/docs/scrots/ui_fd_tab_preproc.png
diff --git a/docs/scrots/ui_fd_tab_qmap.png b/docs/scrots/ui_fd_tab_qmap.png
diff --git a/docs/sec_interface.rst b/docs/sec_interface.rst
@@ -24,7 +24,8 @@ software as a *setpoint* using an active feedback loop.
 The screenshot shows a typical data analysis in PyJibe. A *.jpk-force-map*
 file has been loaded. The plot at the top shows the experimental FD curve
 (approach light blue, retract light red), the model fit (dark blue), and the
-fitting region (shaded yellow). Below are the fit residuals. On the right
+fitting region (white region, bounded by gray background in the upper plot).
+Below are the fit residuals. On the right
 are the main controls (discussed in the sections below). At the bottom
 is the curve list, highlighting which curve is currently shown at the top.
 At the bottom right are the :ref:`curve list controls <sec_ui_fd_curvelist>`.

diff --git a/docs/tutorials/t01_comparison.png b/docs/tutorials/t01_comparison.png
diff --git a/docs/tutorials/t01_fd_compliant.png b/docs/tutorials/t01_fd_compliant.png
diff --git a/docs/tutorials/t01_fd_stiff.png b/docs/tutorials/t01_fd_stiff.png
diff --git a/docs/tutorials/t01_main_init.png b/docs/tutorials/t01_main_init.png
diff --git a/pyjibe/fd/mpl_indent.py b/pyjibe/fd/mpl_indent.py
@@ -14,16 +14,17 @@ def __init__(self):
         """Matplotlib plot for force-indentation data"""
         # Add matplotlib figure
         self.figure = Figure(facecolor="none", tight_layout=True,
-                             frameon={"pad": .0})
+                             frameon=True)
         gs = gridspec.GridSpec(2, 1, height_ratios=[4, 1])
 
         # main axis
         self.axis_main = self.figure.add_subplot(gs[0])
         self.axis_main.grid()
         self.plots = {}
+        self.axis_main.set_facecolor('#DDDDDD')
         self.plots["fit range"] = self.axis_main.axvspan(np.pi,
                                                          np.sqrt(2),
-                                                         facecolor="#FDFDF0",
+                                                         facecolor="#FFFFFF",
                                                          edgecolor="none",
                                                          label="fit range")
         self.plots["approach"] = self.axis_main.plot(range(10),

diff --git a/pyjibe/head/main.py b/pyjibe/head/main.py
@@ -199,7 +199,7 @@ def on_tool_convert(self):
     def load_data(self, files, retry_open=None, separate_analysis=False):
         # approach-retract data files
         supfiles = []
-        for ff in files:
+        for ff in sorted(files):
             path = pathlib.Path(ff)
             if path.suffix in registry.known_suffixes:
                 supfiles.append(ff)

diff --git a/setup.py b/setup.py
@@ -24,7 +24,7 @@
     license="GPL v3",
     description=description,
     long_description=open('README.rst').read() if exists('README.rst') else '',
-    install_requires=["afmformats>=0.12.0",
+    install_requires=["afmformats>=0.12.2",
                       "appdirs",
                       "nanite>=1.6.2",
                       "matplotlib>=3",  # NavigationToolbar2QT mod