-

SciFiReaders/__version__.py

@@ -1,2 +1,2 @@
-version = '0.11.0'
-time = '2023-11-08 17:00:00'
+version = '0.11.5'
+time = '2024-02-26 17:00:00'

SciFiReaders/readers/microscopy/em/tem/dm_reader.py

@@ -196,7 +196,6 @@ def read(self):
             start=1
         channel_number = 0
         for image_number in self.__stored_tags['ImageList'].keys():
-            print(image_number, start)
             if int(image_number) >= start:
                 dataset = self.get_dataset(self.__stored_tags['ImageList'][image_number])
                 if isinstance(dataset, sidpy.Dataset):
@@ -231,8 +230,8 @@ def read(self):
 
         del self.__stored_tags['ImageList'] 
         main_dataset_key = list(self.datasets.keys())[0]
+
         for key, dataset in self.datasets.items():
-            print(key, dataset)
             if 'urvey' in dataset.title:
                 main_dataset_key = key
         if self.verbose:

SciFiReaders/readers/microscopy/em/tem/edax_reader.py

@@ -50,6 +50,7 @@ def reader(h5_file):
     datasets = {}
     # read spectum  images first
     for dataset_item in all_datasets_list:
+        print(dataset_item)
         if 'Live Map' in dataset_item:
             if 'SPD' in dataset_item:
                 dataset = read_spectrum_image(base_group, dataset_item)

SciFiReaders/readers/microscopy/spm/afm/AR_hdf5.py

@@ -95,9 +95,9 @@ def read(self, verbose=False):
             self.channels_name = [name for name in channels_name]
 
         try:
-            self.points_per_sec = np.float(self.note_value('ARDoIVPointsPerSec'))
+            self.points_per_sec = float(self.note_value('ARDoIVPointsPerSec'))
         except NameError:
-            self.points_per_sec = np.float(self.note_value('NumPtsPerSec'))
+            self.points_per_sec = float(self.note_value('NumPtsPerSec'))
 
         if self.verbose:
             print('Map size [X, Y]: ', self.map_size)
@@ -116,11 +116,11 @@ def read(self, verbose=False):
         points_trimmed = np.array(self.segments[:, :, extension_idx]) - short_ext
 
         # Open the output hdf5 file
-        x_dim = np.linspace(0, np.float(self.note_value('FastScanSize')),
+        x_dim = np.linspace(0, float(self.note_value('FastScanSize')),
                             self.map_size['X'])
-        y_dim = np.linspace(0, np.float(self.note_value('FastScanSize')),
+        y_dim = np.linspace(0, float(self.note_value('FastScanSize')),
                             self.map_size['Y'])
-        z_dim = np.arange(tot_length) / np.float(self.points_per_sec)
+        z_dim = np.arange(tot_length) / float(self.points_per_sec)
 
         datasets = [] #list of sidpy datasets
 

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

@@ -14,16 +14,14 @@
 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 ):
+    def read(self):
         """
         Parameters
         ----------
@@ -101,13 +99,13 @@ def read_file_desc(self):
         spectrum_desc = {}
         pspectrum_desc = {}
 
-        with open(self.path,'r', encoding="ISO-8859-1") as f:
+        with open(self.path, 'r', encoding="ISO-8859-1") as f:
 
             lines = f.readlines()
             for index, line in enumerate(lines):
 
                 sline = [val.strip() for val in line.split(':')]
-                #if true, then file describes image.
+                # if true, then file describes image.
 
                 if sline[0].startswith('FileDescBegin'):
                     no_descriptors = 5
@@ -375,60 +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

setup.py

@@ -11,15 +11,17 @@
 
 # TODO: Move requirements to requirements.txt
 requirements = [  # basic
+                'setuptools==58.2.0',
                 'numpy',
                 'toolz',  # dask installation failing without this
                 'cytoolz',  # dask installation failing without this
                 'dask>=2.20.0',
                 'sidpy>=0.11.2',
-                'numba==0.58; python_version < "3.11"',
-                'numba>=0.59.0rc1; python_version >= "3.11"',
+                'numba==0.58; python_version < "3.10"',
+                'numba>=0.59.0rc1; python_version >= "3.10"',
                 'ipython>=7.1.0',
                 'pyUSID',
+                'gdown',
                 # generic:
                 # Reader specific ones go to extras
                ]
@@ -53,10 +55,10 @@
     author_email='[email protected]',
     install_requires=requirements,
     setup_requires=['pytest-runner'],
-    tests_require=['unitest', 'pytest', 'pywget', 'hyperspy', 'pyUSID', 'gwyfile'],
+    tests_require=['pytest', 'pywget', 'hyperspy', 'pyUSID', 'gwyfile', 'gdown'],
     platforms=['Linux', 'Mac OSX', 'Windows 11/10/8.1/8/7'],
     # package_data={'sample':['dataset_1.dat']}
-    test_suite='unittest',
+    test_suite='pytest',
     # dependency='',
     # dependency_links=[''],
     include_package_data=True,

tests/readers/microscopy/spm/afm/test_arhdf5.py

@@ -0,0 +1,34 @@
+import pytest
+import sidpy
+import SciFiReaders as sr
+from pywget import wget
+import os
+import gdown
+try:
+    import gdown
+except ImportError:
+    import pip
+    pip.main(['install', 'gdown'])
+
+@pytest.fixture
+def arhdf5_file():
+    file_path = 'PTO_SS_00.h5'
+    gdown.download('https://drive.google.com/uc?id=10LpXdpm2tPiGEE_rqKlrIkZhaYkP_YBs', file_path, quiet=False)
+    yield file_path
+    os.remove(file_path)
+
+def test_load_test_arhdf5_file(arhdf5_file):
+    data_translator = sr.ARhdf5Reader(arhdf5_file)
+    datasets = data_translator.read(verbose=False)
+    test_data = datasets[1:6]
+    assert len(test_data) == 5, f"Length of dataset should be 5 but is instead {len(test_data)}"
+    channel_names = ['Defl', 'Amp', 'Phase', 'Phas2', 'Freq']
+    channel_units = ['m', 'm', 'deg', 'deg', 'Hz']
+    channel_labels = [['x (m)', 'y (m)', 'z (s)'], ['x (m)', 'y (m)', 'z (s)'], ['x (m)', 'y (m)', 'z (s)'], ['x (m)', 'y (m)', 'z (s)'], ['x (m)', 'y (m)', 'z (s)']]
+    for ind, dataset in enumerate(test_data):
+        assert isinstance(dataset, sidpy.sid.dataset.Dataset), f"Dataset No. {ind} not read in as sidpy dataset but was instead read in as {type(dataset)}"
+        assert dataset.shape[0] == 64, f"Dataset[{ind}] is of size 64 but was read in as {dataset.shape[0]}"
+        assert isinstance(dataset._axes[0], sidpy.sid.dimension.Dimension), "Dataset should have dimension type of sidpy Dimension, but is instead {}".format(type(dataset._axes))
+        assert dataset.quantity == channel_names[ind], "Dataset having inconsistent channel names"
+        assert dataset.units == channel_units[ind], "Dataset having inconsistent unit names"
+        assert dataset.labels == channel_labels[ind], "Dataset having inconsistent channel labels"

tests/readers/microscopy/spm/afm/test_gwy.py

@@ -20,7 +20,7 @@ def gwy_file():
 def test_load_test_gwy_file(gwy_file):
     data_translator = sr.GwyddionReader(gwy_file)
     datasets = data_translator.read(verbose=False)
-    assert len(datasets) == 4, f"Length of dataset should be 2 but is instead {len(datasets)}"
+    assert len(datasets) == 4, f"Length of dataset should be 4 but is instead {len(datasets)}"
     channel_names = ['HeightRetrace', 'AmplitudeRetrace', 'DeflectionRetrace', 'PhaseRetrace']
     channel_units = ['m', 'm', 'm', 'deg']
     channel_labels = [['x (m)', 'y (m)'], ['x (m)', 'y (m)'], ['x (m)', 'y (m)'], ['x (m)', 'y (m)']]