- ref: bump nanite to 1.2.0

 - ref: migrate to afmformats (0.3.0)

CHANGELOG

@@ -1,5 +1,6 @@
 0.5.2
- - ref: bump nanite to 1.2.0 (afmformats)
+ - ref: bump nanite to 1.2.0
+ - ref: migrate to afmformats (0.3.0)
 0.5.1
  - fix: missing title in FD window and missing FD number in export menu
  - enh: add help menu with link to docs, about, and software used (#1)

pyjibe/fd/export.py

@@ -8,7 +8,7 @@
 
 
 def save_tsv_approach_retract(filename, fdist_list, ratings=[]):
-    """Export a list of afmlib.ApproachRetract instances"""
+    """Export fitting results for a list of nanite.Indentation"""
 
     columns = []
 

pyjibe/fd/main.py

@@ -4,9 +4,9 @@
 import pkg_resources
 import time
 
+import afmformats
 import nanite
 import nanite.fit as nfit
-import nanite.read as nread
 import numpy as np
 from PyQt5 import uic, QtCore, QtGui, QtWidgets
 
@@ -144,8 +144,8 @@ def callback(partial):
             try:
                 grp = nanite.IndentationGroup(f, callback=callback)
                 callback(1)
-            except nread.read_jpk_meta.ReadJPKMetaKeyError:
-                # ignore callibration curves
+            except afmformats.errors.FileFormatMetaDataError:
+                # ignore e.g. JPK callibration curves
                 callback(1)
                 continue
             except AbortProgress:
@@ -473,7 +473,7 @@ def on_rating_threshold(self):
             else:
                 it.setCheckState(3, 0)
         # TODO:
-        # -make this more efficient. There is a lot written to disk here.
+        # - make this more efficient. There is a lot written to disk here.
         for fdist in self.data_set:
             self.autosave(fdist)
 

pyjibe/head/custom_widgets.py

@@ -68,14 +68,14 @@ def _icon(self, name):
 
     def save_data(self, *args):
         fname, _e = QtWidgets.QFileDialog.getSaveFileName(
-            self, "Save raw data", "", "Tab Separated Values (*.tsv)")
+            self, "Save raw data", "", "Tab Separated Values (*.tab)")
         if fname:
-            if not fname.endswith(".tsv"):
-                fname += ".tsv"
+            if not fname.endswith(".tab"):
+                fname += ".tab"
             self.save_data_callback(fname)
 
     def save_data_callback(self, filename):
-        """Save the plot data to a tsv file
+        """Save the plot data to a tab file
         """
         raise ValueError("This Method must be overridden!")
 

pyjibe/head/main.py

@@ -7,6 +7,7 @@
 
 from PyQt5 import uic, QtCore, QtWidgets
 
+import afmformats
 import appdirs
 import h5py
 import lmfit
@@ -127,7 +128,7 @@ def on_open_multiple(self, evt=None):
                 self.settings.set_path(dlg.getDirectory(), name="load data")
 
     def on_open_single(self, evt=None):
-        exts = ["*"+e for e in registry.file_extensions]
+        exts = ["*"+e for e in registry.known_suffixes]
         exts_str = "Supported file types ({})".format(" ".join(exts))
         search_dir = self.settings.get_path("load data")
 
@@ -139,7 +140,8 @@ def on_open_single(self, evt=None):
             self.settings.set_path(pathlib.Path(n).parent, name="load data")
 
     def on_software(self):
-        libs = [appdirs,
+        libs = [afmformats,
+                appdirs,
                 h5py,
                 lmfit,
                 matplotlib,
@@ -165,7 +167,7 @@ def load_data(self, files, retry_open=None, separate_analysis=False):
         supfiles = []
         for ff in files:
             path = pathlib.Path(ff)
-            if path.suffix in registry.file_extensions:
+            if path.suffix in registry.known_suffixes:
                 supfiles.append(ff)
 
         # check if AFM files were found

pyjibe/registry.py

@@ -1,11 +1,15 @@
+from afmformats.formats import formats_by_mode
+
 from . import fd
 
 
-analysis_types = {"fd":
-                  {"file extensions": [".jpk", ".jpk-force", ".jpk-force-map"],
-                   "gui": fd.UiForceDistance,
-                   }}
+analysis_types = {
+    "fd": {
+        "suffixes": [f["suffix"] for f in formats_by_mode["force-distance"]],
+        "gui": fd.UiForceDistance,
+        }
+    }
 
-file_extensions = []
+known_suffixes = []
 for _item in analysis_types.values():
-    file_extensions += _item["file extensions"]
+    known_suffixes += _item["suffixes"]

setup.py

@@ -24,7 +24,8 @@
     license="GPL v3",
     description=description,
     long_description=open('README.rst').read() if exists('README.rst') else '',
-    install_requires=["appdirs",
+    install_requires=["afmformats>=0.3.0",
+                      "appdirs",
                       "nanite>=1.2.0",
                       "matplotlib",
                       "pyqt5"],