feat: update pifm.py for 'new' reader rules

The new pycroscopy has switched from Translators to Readers. We no
longer save files in USID or NSID format in order to translate, but
rather translate while reading from the file. The user can choose to
save a given sidpy dataset into USID or NSID format after-the-fact, via
those libraries.

Here, we update the pifm module to match this new standard. As such, we
remove the pyNSID dependencies and the write/create methods which use them.

SciFiReaders/readers/microscopy/spm/afm/pifm.py

@@ -14,14 +14,11 @@
 import numpy as np
 import h5py
 
-from pyNSID.io.hdf_io import write_nsid_dataset
-from pyNSID.io.hdf_io import create_indexed_group, write_simple_attrs
 
-
-class PiFMTranslator(Reader):
+class PiFMReader(Reader):
     """
-    Class that writes images, spectrograms, point spectra and associated ancillary data sets to h5 file in pyUSID data
-    structure.
+    Class that reads images, spectrograms, point spectra and associated
+    ancillary data sets from an Anfatec scan structure.
     """
 
     def read(self):
@@ -376,60 +373,4 @@ def make_dimensions(self):
 
         # self.pos_ind, self.pos_val, self.pos_dims = pos_ind, pos_val, pos_dims
 
-        return 
-
-    # HDF5 creation        
-    def create_hdf5_file(self, append_path='', overwrite=False):
-        """ Sets up the HDF5 file for writing 
-        
-        append_path : string (Optional)
-            h5_file to add these data to, must be a path to the h5_file on disk
-        overwrite : bool (optional, default=False)
-            If True, will overwrite an existing .h5 file of the same name        
-        """
-
-        if not append_path:
-            h5_path = os.path.join(self.directory, self.basename.replace('.txt', '.h5'))
-            if os.path.exists(h5_path):
-                if not overwrite:
-                    raise FileExistsError('This file already exists). Set attribute overwrite to True')
-                else:
-                    print('Overwriting file', h5_path)
-                    #os.remove(h5_path)
-
-            self.h5_f = h5py.File(h5_path, mode='w')
-
-        else:
-            if not os.path.exists(append_path):
-                raise Exception('File does not exist. Check pathname.')
-            self.h5_f = h5py.File(append_path, mode='r+')
-
-        self.h5_img_grp = create_indexed_group(self.h5_f, "Images")
-        self.h5_spectra_grp = create_indexed_group(self.h5_f, "Spectra")
-        self.h5_spectrogram_grp = create_indexed_group(self.h5_f, "Spectrogram")
-
-        write_simple_attrs(self.h5_img_grp, self.params_dictionary)
-        write_simple_attrs(self.h5_spectra_grp, self.params_dictionary)
-        write_simple_attrs(self.h5_spectrogram_grp, self.params_dictionary)
-
         return
-
-    def write_datasets_hdf5(self):
-        """ Writes the datasets as pyNSID datasets to the HDF5 file"""
-        for dset in self.datasets:
-
-            if 'IMAGE' in dset.data_type.name:
-
-                write_nsid_dataset(dset, self.h5_img_grp)
-
-            elif 'SPECTRUM' in dset.data_type.name:
-
-                write_nsid_dataset(dset, self.h5_spectra_grp) 
-
-            else:
-
-                write_nsid_dataset(dset, self.h5_spectrogram_grp) 
-
-        self.h5_f.file.close()    
-
-        return