diff --git a/setup.py b/setup.py index ab30a4a..b902441 100644 --- a/setup.py +++ b/setup.py @@ -34,6 +34,8 @@ 'spectral.utilities'], package_data={'spectral.tests': ['data/*.spc', 'data/ecostress/*.txt', + 'data/relab/data/mem/mm/*.txt', + 'data/relab/data/mem/mm/*.asc', 'data/usgs/ASCIIdata/liba/*.txt', 'data/usgs/ASCIIdata/liba/ChapterB_b0/*.txt', 'data/usgs/ASCIIdata/liba/ChapterD_d0/*.txt', diff --git a/spectral/database/__init__.py b/spectral/database/__init__.py index 26e0499..3456543 100644 --- a/spectral/database/__init__.py +++ b/spectral/database/__init__.py @@ -2,4 +2,5 @@ from .aster import AsterDatabase from .ecostress import EcostressDatabase +from .relab import RelabDatabase from .usgs import USGSDatabase diff --git a/spectral/database/relab.py b/spectral/database/relab.py new file mode 100644 index 0000000..e0c4eaf --- /dev/null +++ b/spectral/database/relab.py @@ -0,0 +1,484 @@ +''' +Code for reading and managing relab spectral library data. +''' + +from __future__ import absolute_import, division, print_function, unicode_literals + +from spectral.utilities.python23 import IS_PYTHON3, tobytes, frombytes + +from .spectral_database import SpectralDatabase + +if IS_PYTHON3: + readline = lambda fin: fin.readline() + open_file = lambda filename: open(filename, encoding='iso-8859-1') +else: + readline = lambda fin: fin.readline().decode('iso-8859-1') + open_file = lambda filename: open(filename) + +table_schemas = [ + 'CREATE TABLE Samples (SampleID INTEGER PRIMARY KEY, Name TEXT, Type TEXT, Class TEXT, SubClass TEXT, ' + 'ParticleSize TEXT, SampleNum TEXT, Owner TEXT, Origin TEXT, Phase TEXT, Description TEXT)', + 'CREATE TABLE Spectra (SpectrumID INTEGER PRIMARY KEY, SampleID INTEGER, SensorCalibrationID INTEGER, ' + 'Instrument TEXT, Environment TEXT, Measurement TEXT, ' + 'XUnit TEXT, YUnit TEXT, MinWavelength FLOAT, MaxWavelength FLOAT, ' + 'NumValues INTEGER, XData BLOB, YData BLOB)', +] + +arraytypecode = chr(ord('f')) + +# These files contained malformed signature data and will be ignored. +bad_files = [ + 'jhu.nicolet.mineral.silicate.tectosilicate.fine.albite1.spectrum.txt', + 'usgs.perknic.rock.igneous.mafic.colid.me3.spectrum.txt' +] + + +def read_pair(fin, num_lines=1): + '''Reads a colon-delimited attribute-value pair from the file stream.''' + s = '' + for i in range(num_lines): + s += " " + readline(fin).strip() + return [x.strip().lower() for x in s.split(':')] + + +class Signature: + '''Object to store sample/measurement metadata, as well as wavelength-signature vectors.''' + def __init__(self): + self.sample = {} + self.measurement = {} + + +def read_relab_file(filename): + '''Reads a relab spectrum file.''' + with open_file(filename) as fin: + lines = [line.rstrip('\n') for line in fin] + + s = Signature() + + # Read signature spectrum + pairs = [] + # Start line counter + count = 0 + # Extract ReLab ID and store it + relab_id = int(lines[0]) + s.sample["relab_id"] = relab_id + s.measurement["relab_id"] = relab_id + count = count + 1 + # Extract central wavelengths and reflectances + for c in range(count, len(lines)): + if (lines[c] != ""): + out = lines[c].strip().split(" ") + # Remove empty slots + out1 = list(filter(None, out)) + #print(out1[0].strip(), out1[1].strip()) + pair = [float(out1[0].strip()), float(out1[1].strip())] + pairs.append(pair) + else: + break + + # Update line count + count = count + c + + [x, y] = [list(v) for v in zip(*pairs)] + + # Make sure wavelengths are ascending + if float(x[0]) > float(x[-1]): + x.reverse() + y.reverse() + s.x = [float(val) for val in x] + s.y = [float(val) for val in y] + s.measurement['first x value'] = x[0] + s.measurement['last x value'] = x[-1] + s.measurement['number of x values'] = len(x) + + # Extract Metadata + # Read sample metadata + #pair = read_pair(fin, lpv[i]) + #s.sample[pair[0].lower()] = pair[1] + + # Read measurement metadata + #pair = read_pair(fin, lpv[i]) + #s.measurement[pair[0].lower()] = pair[1] + + m = [] + description = "" + stage = None + + while (lines[count].strip() == ""): + count = count + 1 + + # Filename extraction + if(stage == None and lines[count].strip() != ""): + # Remove heading and trailing spaces + ml = lines[count].strip() + if '.ASC' in ml: + fname = ml.replace(' ','') + m.append(fname) + s.sample["name"] = str(fname) + #print("File NAME %s" % (fname)) + stage = "ASC" + + count = count + 1 + ml = lines[count].strip() + + while (lines[count].strip() == ""): + count = count + 1 + + # Extract Material Name after Filename extraction + if(stage == "ASC" and lines[count].strip() != ""): + ml = lines[count].strip() + #print("Material NAME %s" % (ml)) + s.measurement['name'] = str(ml) + stage = "name" + + count = count + 1 + ml = lines[count].strip() + + while (lines[count].strip() == ""): + count = count + 1 + + if(lines[count].strip() != ""): + ml = lines[count].strip() + # Extract seprately date and time + if 'Date' in ml: + date = ml.split('Time:')[0] + time = ml.split('Time:')[-1] + s.sample["date"] = date.replace('Date:',"").replace(" "," ").strip() + s.sample["time"] = time + # Extract Source and Detection Angles & Voltage + elif 'Volt' in ml: + volt = ml.split('Volt:')[-1] + dang = ml.split('Volt:')[-2] + dang1 = dang.split('Detect Ang:')[-1] + sang = dang.split('Detect Ang:')[-2] + s.measurement['source_angle'] = sang.replace("Source Ang:","").strip() + s.measurement['detect_angle'] = dang1.strip() + s.measurement['volt'] = volt + # All other cases + else: + description += ml + " " + s.sample['description'] = description + " " + s.measurement['name'] + else: + while (lines[count].strip() == ""): + count = count + 1 + ml = lines[count].strip() + + return s + + +class RelabDatabase(SpectralDatabase): + '''A relational database to manage relab spectral library data.''' + schemas = table_schemas + + def _add_sample(self, name, sampleType, sampleClass, subClass, + particleSize, sampleNumber, owner, origin, phase, + description): + sql = '''INSERT INTO Samples (Name, Type, Class, SubClass, ParticleSize, SampleNum, Owner, Origin, Phase, Description) + VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)''' + self.cursor.execute(sql, (name, sampleType, sampleClass, subClass, + particleSize, sampleNumber, owner, origin, + phase, description)) + rowId = self.cursor.lastrowid + self.db.commit() + return rowId + + def _add_signature( + self, sampleID, calibrationID, instrument, environment, measurement, + xUnit, yUnit, minWavelength, maxWavelength, xData, yData): + import sqlite3 + import array + sql = '''INSERT INTO Spectra (SampleID, SensorCalibrationID, Instrument, + Environment, Measurement, XUnit, YUnit, MinWavelength, MaxWavelength, + NumValues, XData, YData) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)''' + xBlob = sqlite3.Binary(tobytes(array.array(arraytypecode, xData))) + yBlob = sqlite3.Binary(tobytes(array.array(arraytypecode, yData))) + numValues = len(xData) + self.cursor.execute( + sql, ( + sampleID, calibrationID, instrument, environment, measurement, + xUnit, yUnit, minWavelength, maxWavelength, numValues, xBlob, + yBlob)) + rowId = self.cursor.lastrowid + self.db.commit() + return rowId + + @classmethod + def create(cls, filename, relab_data_dir=None): + '''Creates an relab relational database by parsing RELAB data files. + + Arguments: + + `filename` (str): + + Name of the new sqlite database file to create. + + `relab_data_dir` (str): + + Path to the directory containing relab library data files. If + this argument is not provided, no data will be imported. + + Returns: + + An :class:`~spectral.database.RelabDatabase` object. + + Example:: + + >>> RelabDatabase.create("relab_lib.db", "/STORAGE/ReLab/data") + + This is a class method (it does not require instantiating an + RelabDatabase object) that creates a new database by parsing all of the + files in the relab library data directory. Normally, this should only + need to be called once. Subsequently, a corresponding database object + can be created by instantiating a new RelabDatabase object with the + path the database file as its argument. For example:: + + >>> from spectral.database.relab import RelabDatabase + >>> db = RelabDatabase("relab_lib.db") + ''' + import os + if os.path.isfile(filename): + raise Exception('Error: Specified file already exists.') + db = cls() + db._connect(filename) + for schema in cls.schemas: + db.cursor.execute(schema) + if relab_data_dir: + db._import_files(relab_data_dir) + return db + + def __init__(self, sqlite_filename=None): + '''Creates a database object to interface an existing database. + + Arguments: + + `sqlite_filename` (str): + + Name of the database file. If this argument is not provided, + an interface to a database file will not be established. + + Returns: + + An :class:`~spectral.RelabDatabase` connected to the database. + ''' + from spectral.io.spyfile import find_file_path + if sqlite_filename: + self._connect(find_file_path(sqlite_filename)) + else: + self.db = None + self.cursor = None + + def read_file(self, filename): + return read_relab_file(filename) + + def _import_files(self, data_dir, ignore=bad_files): + '''Read each file in the relab library and convert to AVIRIS bands.''' + from glob import glob + import numpy + import os + + if not os.path.isdir(data_dir): + raise Exception('Error: Invalid directory name specified.') + if ignore is not None: + filesToIgnore = [data_dir + '/' + f for f in ignore] + else: + filesToIgnore = [] + + numFiles = 0 + numIgnored = 0 + + sigID = 1 + + class Sig: + pass + sigs = [] + + # Get all .asc files in subsubdirs + files = glob(data_dir+'/**/*/*.asc', recursive=True) + print(len(files)) + + for f in range(len(files)): + print('Importing %s.' % files[f]) + try: + sig = self.read_file(files[f]) + s = sig.sample + sampleNum = s['relab_id'] + except: + raise Exception ('Error creating SIG' % (files[f])) + + phase = 'solid' + s['type'] = "manmade_natural" + s['class'] = " " + s['subclass'] = " " + s['particle size'] = " " + s['owner'] = " " + s['origin'] = "RELab" + try: + idd = self._add_sample(s['name'], s['type'], s['class'], s['subclass'], s['particle size'], + sampleNum, s['owner'], s['origin'], phase, s['description']) + except: + raise Exception ('Error creating IDD') + + instrument = os.path.basename(files[f]).split('.')[0] + environment = 'lab' + m = sig.measurement + + # Correct numerous mispellings of "reflectance" and "transmittance" + m['y units'] = 'reflectance (percent)' + yUnit = m['y units'] + measurement = 'reflectance' + m['x units'] = 'wavelength (nm)' + try: + self._add_signature(idd, -1, instrument, environment, measurement, + m['x units'], yUnit, m['first x value'], + m['last x value'], sig.x, sig.y) + except: + raise Exception ('Error creating Signature') + + if numFiles == 0: + print('No data files were found in directory "%s".' % data_dir) + else: + print('Processed %d files.' % numFiles) + if numIgnored > 0: + print('Ignored the following %d bad files:' % (numIgnored)) + for f in filesToIgnore: + print('\t' + f) + + return sigs + + def get_spectrum(self, spectrumID): + '''Returns a spectrum from the database. + + Usage: + + (x, y) = relab.get_spectrum(spectrumID) + + Arguments: + + `spectrumID` (int): + + The **SpectrumID** value for the desired spectrum from the + **Spectra** table in the database. + + Returns: + + `x` (list): + + Band centers for the spectrum. + + `y` (list): + + Spectrum data values for each band. + + Returns a pair of vectors containing the wavelengths and measured + values values of a measurment. For additional metadata, call + "get_signature" instead. + ''' + import array + query = '''SELECT XData, YData FROM Spectra WHERE SpectrumID = ?''' + result = self.cursor.execute(query, (spectrumID,)) + rows = result.fetchall() + if len(rows) < 1: + raise 'Measurement record not found' + x = array.array(arraytypecode) + frombytes(x, rows[0][0]) + y = array.array(arraytypecode) + frombytes(y, rows[0][1]) + return (list(x), list(y)) + + def get_signature(self, spectrumID): + '''Returns a spectrum with some additional metadata. + + Usage:: + + sig = relab.get_signature(spectrumID) + + Arguments: + + `spectrumID` (int): + + The **SpectrumID** value for the desired spectrum from the + **Spectra** table in the database. + + Returns: + + `sig` (:class:`~spectral.database.relab.Signature`): + + An object with the following attributes: + + ============== ===== ======================================== + Attribute Type Description + ============== ===== ======================================== + measurement_id int SpectrumID value from Spectra table + sample_name str **Sample** from the **Samples** table + sample_id int **SampleID** from the **Samples** table + x list list of band center wavelengths + y list list of spectrum values for each band + ============== ===== ======================================== + ''' + import array + + # Retrieve spectrum from Spectra table + query = '''SELECT Samples.Name, Samples.SampleID, XData, YData + FROM Samples, Spectra WHERE Samples.SampleID = Spectra.SampleID + AND Spectra.SpectrumID = ?''' + result = self.cursor.execute(query, (spectrumID,)) + results = result.fetchall() + if len(results) < 1: + raise "Measurement record not found" + + sig = Signature() + sig.measurement_id = spectrumID + sig.sample_name = results[0][0] + sig.sample_id = results[0][1] + x = array.array(arraytypecode) + frombytes(x, results[0][2]) + sig.x = list(x) + y = array.array(arraytypecode) + frombytes(y, results[0][3]) + sig.y = list(y) + return sig + + def create_envi_spectral_library(self, spectrumIDs, bandInfo): + '''Creates an ENVI-formatted spectral library for a list of spectra. + + Arguments: + + `spectrumIDs` (list of ints): + + List of **SpectrumID** values for of spectra in the "Spectra" + table of the relab database. + + `bandInfo` (:class:`~spectral.BandInfo`): + + The spectral bands to which the original relab library spectra + will be resampled. + + Returns: + + A :class:`~spectral.io.envi.SpectralLibrary` object. + + The IDs passed to the method should correspond to the SpectrumID field + of the relab database "Spectra" table. All specified spectra will be + resampled to the same discretization specified by the bandInfo + parameter. See :class:`spectral.BandResampler` for details on the + resampling method used. + ''' + from spectral.algorithms.resampling import BandResampler + from spectral.io.envi import SpectralLibrary + import numpy + import unicodedata + spectra = numpy.empty((len(spectrumIDs), len(bandInfo.centers))) + names = [] + for i in range(len(spectrumIDs)): + sig = self.get_signature(spectrumIDs[i]) + resample = BandResampler( + sig.x, bandInfo.centers, None, bandInfo.bandwidths) + spectra[i] = resample(sig.y) + names.append(unicodedata.normalize('NFKD', sig.sample_name). + encode('ascii', 'ignore')) + header = {} + header['wavelength units'] = 'um' + header['spectra names'] = names + header['wavelength'] = bandInfo.centers + header['fwhm'] = bandInfo.bandwidths + return SpectralLibrary(spectra, header, {}) diff --git a/spectral/tests/data/relab/data/mem/mm/bkr1mm074ws.asc b/spectral/tests/data/relab/data/mem/mm/bkr1mm074ws.asc new file mode 100644 index 0000000..f792768 --- /dev/null +++ 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diff --git a/spectral/tests/database.py b/spectral/tests/database.py index 4a27a39..16bac3e 100644 --- a/spectral/tests/database.py +++ b/spectral/tests/database.py @@ -23,6 +23,9 @@ ECOSTRESS_DATA_DIR = os.path.join(os.path.split(__file__)[0], 'data/ecostress') ECOSTRESS_DB = os.path.join(testdir, 'ecostress.db') +RELAB_DATA_DIR = os.path.join(os.path.split(__file__)[0], + 'data/relab/data/') +RELAB_DB = os.path.join(testdir, 'relab.db') USGS_DATA_DIR = os.path.join(os.path.split(__file__)[0], 'data/usgs/ASCIIdata') USGS_DB = os.path.join(testdir, 'usgs.db') @@ -71,6 +74,35 @@ def test_create_envi_lib(self): slib = self.db.create_envi_spectral_library(ids, bands) assert(slib.spectra.shape == (3, 220)) +class RELABDatabaseCreationTest(SpyTest): + '''Tests RELAB database creation from text files.''' + + def __init__(self): + pass + + def setup(self): + if not os.path.isdir(testdir): + os.makedirs(testdir) + if os.path.exists(RELAB_DB): + os.remove(RELAB_DB) + + def test_create_database(self): + '''Test creating new database from RELAB data files.''' + db = spy.RelabDatabase.create(RELAB_DB, RELAB_DATA_DIR) + assert(list(db.query('SELECT COUNT() FROM Spectra'))[0][0] == 1) + +class RELABDatabaseTest(SpyTest): + '''Tests that RELAB database works properly''' + + def __init__(self): + pass + + def setup(self): + self.db = spy.RelabDatabase(RELAB_DB) + + def test_read_signatures(self): + '''Can get spectra from the opened database.''' + assert(list(self.db.query('SELECT COUNT() FROM Spectra'))[0][0] == 1) class USGSDatabaseCreationTest(SpyTest): '''Tests USGS database creation from text files.''' @@ -164,7 +196,9 @@ def run(): print('\n' + '-' * 72) print('Running database tests.') print('-' * 72) - for T in [ECOSTRESSDatabaseCreationTest, ECOSTRESSDatabaseTest, USGSDatabaseCreationTest, USGSDatabaseTest]: + for T in [ECOSTRESSDatabaseCreationTest, ECOSTRESSDatabaseTest, \ + RELABDatabaseCreationTest, RELABDatabaseTest, \ + USGSDatabaseCreationTest, USGSDatabaseTest]: T().run()