enh: support mirroring the input directory structure in the data conv…

…ersion tool (close #29)

CHANGELOG

@@ -1,3 +1,6 @@
+0.14.2
+ - enh: support mirroring the input directory structure in the data
+   conversion tool (#29)
 0.14.1
  - maintenance release
 0.14.0

pyjibe/head/dlg_tool_convert.py

@@ -24,6 +24,7 @@ def __init__(self, parent, *args, **kwargs):
         self.toolButton_clear.clicked.connect(self._file_list.clear)
 
     def _convert_merge(self):
+        """Merge all curves into one HDF5 file"""
         file, _ = QtWidgets.QFileDialog.getSaveFileName(
             self.parent(),
             "Output file",
@@ -43,7 +44,55 @@ def _convert_merge(self):
                                  fmt="hdf5")
         return True
 
+    def _convert_mirror(self):
+        """Mirror input file and directory strucutre to output (HDF5 only)"""
+        out_dir = QtWidgets.QFileDialog.getExistingDirectory(
+            self.parent(), "Select output directory", "")
+        if out_dir:
+            out_dir = pathlib.Path(out_dir)
+            # Determine the common input path of all files
+            # TODO:
+            #  This will not work with files on different drives under
+            #  Windows.
+            pc = str(self.file_list[0])
+            for pp in self.file_list[1:]:
+                pc = "".join(
+                    [a for (a, b) in zip(str(pp[:len(pc)]), pc) if a == b])
+            pc = pathlib.Path(pc)
+            if not pc.exists():
+                # There is probably just a piece of a file name stem left
+                pc = pc.parent
+            assert pc.exists()
+            # Create a output path list
+            out_list = []
+            for pp in self.file_list:
+                pp = pathlib.Path(pp)
+                relp = pp.relative_to(pc)
+                outp = (out_dir / relp).with_suffix(".h5")
+                if outp in out_list:
+                    ii = 2
+                    while True:
+                        new = outp.with_name(f"{outp.stem}-{ii}.h5")
+                        if new not in out_list:
+                            outp = new
+                            break
+                        ii += 1
+                out_list.append(outp)
+            # Perform the export
+            for pin, pout in zip(self.file_list, out_list):
+                pout.parent.mkdir(parents=True, exist_ok=True)
+                with h5py.File(pout, mode="w") as h5:
+                    fdlist = afmformats.load_data(pin)
+                    for fdist in fdlist:
+                        fdist.export(h5,
+                                     metadata=self.get_metadata_keys(fdist),
+                                     fmt="hdf5")
+            return True
+        else:
+            return False
+
     def _convert_curve(self):
+        """Output all files into one directory, one file per curve"""
         out_dir = QtWidgets.QFileDialog.getExistingDirectory(
             self.parent(), "Select output directory", "")
         if out_dir:
@@ -64,6 +113,7 @@ def _convert_curve(self):
             return False  # do not close the dialog
 
     def _convert_unaltered(self):
+        """Output all files into one directory (HDF5 only)"""
         out_dir = QtWidgets.QFileDialog.getExistingDirectory(
             self.parent(), "Select output directory", "")
         if out_dir:
@@ -109,6 +159,8 @@ def convert(self):
             return self._convert_unaltered()
         elif self.radioButton_merge.isChecked():
             return self._convert_merge()
+        elif self.radioButton_mirror.isChecked():
+            return self._convert_mirror()
         else:
             return self._convert_curve()
 

pyjibe/head/dlg_tool_convert.ui

@@ -6,8 +6,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>532</width>
-    <height>477</height>
+    <width>536</width>
+    <height>535</height>
    </rect>
   </property>
   <property name="acceptDrops">
@@ -70,7 +70,7 @@
      <property name="topMargin">
       <number>0</number>
      </property>
-     <item row="1" column="0">
+     <item row="1" column="0" alignment="Qt::AlignTop">
       <widget class="QLabel" name="label_3">
        <property name="text">
         <string>File grouping:</string>
@@ -79,7 +79,7 @@
      </item>
      <item row="1" column="1">
       <widget class="QWidget" name="widget_group" native="true">
-       <layout class="QHBoxLayout" name="horizontalLayout_2">
+       <layout class="QVBoxLayout" name="verticalLayout_2">
         <property name="leftMargin">
          <number>0</number>
         </property>
@@ -92,36 +92,46 @@
         <property name="bottomMargin">
          <number>0</number>
         </property>
+        <item>
+         <widget class="QRadioButton" name="radioButton_mirror">
+          <property name="text">
+           <string>mirror original file names and directory structure</string>
+          </property>
+          <property name="checked">
+           <bool>true</bool>
+          </property>
+         </widget>
+        </item>
         <item>
          <widget class="QRadioButton" name="radioButton_unaltered">
           <property name="toolTip">
            <string>Each input file is converted to one output file</string>
           </property>
           <property name="text">
-           <string>unaltered</string>
+           <string>save all files into one directory</string>
           </property>
           <property name="checked">
-           <bool>true</bool>
+           <bool>false</bool>
           </property>
          </widget>
         </item>
         <item>
-         <widget class="QRadioButton" name="radioButton_merge">
+         <widget class="QRadioButton" name="radioButton_onefile">
           <property name="toolTip">
-           <string>All input data are merged into one output file</string>
+           <string>Input files with more than one dataset produce more output files</string>
           </property>
           <property name="text">
-           <string>merge all</string>
+           <string>save all files into one directory, one file per curve</string>
           </property>
          </widget>
         </item>
         <item>
-         <widget class="QRadioButton" name="radioButton_onefile">
+         <widget class="QRadioButton" name="radioButton_merge">
           <property name="toolTip">
-           <string>Input files with more than one dataset produce more output files</string>
+           <string>All input data are merged into one output file</string>
           </property>
           <property name="text">
-           <string>one file per curve</string>
+           <string>merge all files into one HDF5 file</string>
           </property>
          </widget>
         </item>
@@ -279,16 +289,16 @@
   <connection>
    <sender>radioButton_hdf5</sender>
    <signal>toggled(bool)</signal>
-   <receiver>radioButton_unaltered</receiver>
+   <receiver>radioButton_mirror</receiver>
    <slot>setChecked(bool)</slot>
    <hints>
     <hint type="sourcelabel">
      <x>375</x>
      <y>366</y>
     </hint>
     <hint type="destinationlabel">
-     <x>166</x>
-     <y>395</y>
+     <x>299</x>
+     <y>366</y>
     </hint>
    </hints>
   </connection>