def test_types(self):
key_c = Key('C')
self.assertEqual(IonianScale, key_c.ionian_mode.base_scale)
self.assertTrue(isinstance(key_c.ionian_mode, Mode))
c_ionian_mode = Mode(C, IonianScale)
self.assertEqual(IonianScale, c_ionian_mode.base_scale)
self.assertTrue(isinstance(c_ionian_mode, Mode))
def test_dorian__sharp_tonics(self):
self.assertEqual(('C#', 'D#', 'E', 'F#', 'G#', 'A#', 'B'),
Mode(C_sharp, DorianScale).notes)
self.assertEqual(('D#', 'E#', 'F#', 'G#', 'A#', 'B#', 'C#'),
Mode(D_sharp, DorianScale).notes)
self.assertEqual(('E#', 'F##', 'G#', 'A#', 'B#', 'C##', 'D#'),
Mode(E_sharp, DorianScale).notes)
self.assertEqual(('F#', 'G#', 'A', 'B', 'C#', 'D#', 'E'),
Mode(F_sharp, DorianScale).notes)
self.assertEqual(('G#', 'A#', 'B', 'C#', 'D#', 'E#', 'F#'),
Mode(G_sharp, DorianScale).notes)
self.assertEqual(('A#', 'B#', 'C#', 'D#', 'E#', 'F##', 'G#'),
Mode(A_sharp, DorianScale).notes)
self.assertEqual(('B#', 'C##', 'D#', 'E#', 'F##', 'G##', 'A#'),
Mode(B_sharp, DorianScale).notes)
def test_dorian__natural_tonics(self):
self.assertEqual(('C', 'D', 'Eb', 'F', 'G', 'A', 'Bb'),
Mode(C, DorianScale).notes)
self.assertEqual(('D', 'E', 'F', 'G', 'A', 'B', 'C'),
Mode(D, DorianScale).notes)
self.assertEqual(('E', 'F#', 'G', 'A', 'B', 'C#', 'D'),
Mode(E, DorianScale).notes)
self.assertEqual(('F', 'G', 'Ab', 'Bb', 'C', 'D', 'Eb'),
Mode(F, DorianScale).notes)
self.assertEqual(('G', 'A', 'Bb', 'C', 'D', 'E', 'F'),
Mode(G, DorianScale).notes)
self.assertEqual(('A', 'B', 'C', 'D', 'E', 'F#', 'G'),
Mode(A, DorianScale).notes)
self.assertEqual(('B', 'C#', 'D', 'E', 'F#', 'G#', 'A'),
Mode(B, DorianScale).notes)
def test_ionian__flat_tonics(self):
self.assertEqual(('Cb', 'Db', 'Eb', 'Fb', 'Gb', 'Ab', 'Bb'),
Mode(C_flat, IonianScale).notes)
self.assertEqual(('Db', 'Eb', 'F', 'Gb', 'Ab', 'Bb', 'C'),
Mode(D_flat, IonianScale).notes)
self.assertEqual(('Eb', 'F', 'G', 'Ab', 'Bb', 'C', 'D'),
Mode(E_flat, IonianScale).notes)
self.assertEqual(('Fb', 'Gb', 'Ab', 'Bbb', 'Cb', 'Db', 'Eb'),
Mode(F_flat, IonianScale).notes)
self.assertEqual(('Gb', 'Ab', 'Bb', 'Cb', 'Db', 'Eb', 'F'),
Mode(G_flat, IonianScale).notes)
self.assertEqual(('Ab', 'Bb', 'C', 'Db', 'Eb', 'F', 'G'),
Mode(A_flat, IonianScale).notes)
self.assertEqual(('Bb', 'C', 'D', 'Eb', 'F', 'G', 'A'),
Mode(B_flat, IonianScale).notes)
def test_locrian__flat_tonics(self):
self.assertEqual(('Cb', 'Dbb', 'Ebb', 'Fb', 'Gbb', 'Abb', 'Bbb'),
Mode(C_flat, LocrianScale).notes)
self.assertEqual(('Db', 'Ebb', 'Fb', 'Gb', 'Abb', 'Bbb', 'Cb'),
Mode(D_flat, LocrianScale).notes)
self.assertEqual(('Eb', 'Fb', 'Gb', 'Ab', 'Bbb', 'Cb', 'Db'),
Mode(E_flat, LocrianScale).notes)
self.assertEqual(('Fb', 'Gbb', 'Abb', 'Bbb', 'Cbb', 'Dbb', 'Ebb'),
Mode(F_flat, LocrianScale).notes)
self.assertEqual(('Gb', 'Abb', 'Bbb', 'Cb', 'Dbb', 'Ebb', 'Fb'),
Mode(G_flat, LocrianScale).notes)
self.assertEqual(('Ab', 'Bbb', 'Cb', 'Db', 'Ebb', 'Fb', 'Gb'),
Mode(A_flat, LocrianScale).notes)
self.assertEqual(('Bb', 'Cb', 'Db', 'Eb', 'Fb', 'Gb', 'Ab'),
Mode(B_flat, LocrianScale).notes)
def test_locrian__natural_tonics(self):
self.assertEqual(('C', 'Db', 'Eb', 'F', 'Gb', 'Ab', 'Bb'),
Mode(C, LocrianScale).notes)
self.assertEqual(('D', 'Eb', 'F', 'G', 'Ab', 'Bb', 'C'),
Mode(D, LocrianScale).notes)
self.assertEqual(('E', 'F', 'G', 'A', 'Bb', 'C', 'D'),
Mode(E, LocrianScale).notes)
self.assertEqual(('F', 'Gb', 'Ab', 'Bb', 'Cb', 'Db', 'Eb'),
Mode(F, LocrianScale).notes)
self.assertEqual(('G', 'Ab', 'Bb', 'C', 'Db', 'Eb', 'F'),
Mode(G, LocrianScale).notes)
self.assertEqual(('A', 'Bb', 'C', 'D', 'Eb', 'F', 'G'),
Mode(A, LocrianScale).notes)
self.assertEqual(('B', 'C', 'D', 'E', 'F', 'G', 'A'),
Mode(B, LocrianScale).notes)
def test_ionian__natural_tonics(self):
self.assertEqual(('C', 'D', 'E', 'F', 'G', 'A', 'B'),
Mode(C, IonianScale).notes)
self.assertEqual(('D', 'E', 'F#', 'G', 'A', 'B', 'C#'),
Mode(D, IonianScale).notes)
self.assertEqual(('E', 'F#', 'G#', 'A', 'B', 'C#', 'D#'),
Mode(E, IonianScale).notes)
self.assertEqual(('F', 'G', 'A', 'Bb', 'C', 'D', 'E'),
Mode(F, IonianScale).notes)
self.assertEqual(('G', 'A', 'B', 'C', 'D', 'E', 'F#'),
Mode(G, IonianScale).notes)
self.assertEqual(('A', 'B', 'C#', 'D', 'E', 'F#', 'G#'),
Mode(A, IonianScale).notes)
self.assertEqual(('B', 'C#', 'D#', 'E', 'F#', 'G#', 'A#'),
Mode(B, IonianScale).notes)
def test_mixolydian__natural_tonics(self):
self.assertEqual(('C', 'D', 'E', 'F', 'G', 'A', 'Bb'),
Mode(C, MixolydianScale).notes)
self.assertEqual(('D', 'E', 'F#', 'G', 'A', 'B', 'C'),
Mode(D, MixolydianScale).notes)
self.assertEqual(('E', 'F#', 'G#', 'A', 'B', 'C#', 'D'),
Mode(E, MixolydianScale).notes)
self.assertEqual(('F', 'G', 'A', 'Bb', 'C', 'D', 'Eb'),
Mode(F, MixolydianScale).notes)
self.assertEqual(('G', 'A', 'B', 'C', 'D', 'E', 'F'),
Mode(G, MixolydianScale).notes)
self.assertEqual(('A', 'B', 'C#', 'D', 'E', 'F#', 'G'),
Mode(A, MixolydianScale).notes)
self.assertEqual(('B', 'C#', 'D#', 'E', 'F#', 'G#', 'A'),
Mode(B, MixolydianScale).notes)
def test_lydian__natural_tonics(self):
self.assertEqual(('C', 'D', 'E', 'F#', 'G', 'A', 'B'),
Mode(C, LydianScale).notes)
self.assertEqual(('D', 'E', 'F#', 'G#', 'A', 'B', 'C#'),
Mode(D, LydianScale).notes)
self.assertEqual(('E', 'F#', 'G#', 'A#', 'B', 'C#', 'D#'),
Mode(E, LydianScale).notes)
self.assertEqual(('F', 'G', 'A', 'B', 'C', 'D', 'E'),
Mode(F, LydianScale).notes)
self.assertEqual(('G', 'A', 'B', 'C#', 'D', 'E', 'F#'),
Mode(G, LydianScale).notes)
self.assertEqual(('A', 'B', 'C#', 'D#', 'E', 'F#', 'G#'),
Mode(A, LydianScale).notes)
self.assertEqual(('B', 'C#', 'D#', 'E#', 'F#', 'G#', 'A#'),
Mode(B, LydianScale).notes)
def test_phrygian__natural_tonics(self):
self.assertEqual(('C', 'Db', 'Eb', 'F', 'G', 'Ab', 'Bb'),
Mode(C, PhrygianScale).notes)
self.assertEqual(('D', 'Eb', 'F', 'G', 'A', 'Bb', 'C'),
Mode(D, PhrygianScale).notes)
self.assertEqual(('E', 'F', 'G', 'A', 'B', 'C', 'D'),
Mode(E, PhrygianScale).notes)
self.assertEqual(('F', 'Gb', 'Ab', 'Bb', 'C', 'Db', 'Eb'),
Mode(F, PhrygianScale).notes)
self.assertEqual(('G', 'Ab', 'Bb', 'C', 'D', 'Eb', 'F'),
Mode(G, PhrygianScale).notes)
self.assertEqual(('A', 'Bb', 'C', 'D', 'E', 'F', 'G'),
Mode(A, PhrygianScale).notes)
self.assertEqual(('B', 'C', 'D', 'E', 'F#', 'G', 'A'),
Mode(B, PhrygianScale).notes)
def test_aeolian__natural_tonics(self):
self.assertEqual(('C', 'D', 'Eb', 'F', 'G', 'Ab', 'Bb'),
Mode(C, AeolianScale).notes)
self.assertEqual(('D', 'E', 'F', 'G', 'A', 'Bb', 'C'),
Mode(D, AeolianScale).notes)
self.assertEqual(('E', 'F#', 'G', 'A', 'B', 'C', 'D'),
Mode(E, AeolianScale).notes)
self.assertEqual(('F', 'G', 'Ab', 'Bb', 'C', 'Db', 'Eb'),
Mode(F, AeolianScale).notes)
self.assertEqual(('G', 'A', 'Bb', 'C', 'D', 'Eb', 'F'),
Mode(G, AeolianScale).notes)
self.assertEqual(('A', 'B', 'C', 'D', 'E', 'F', 'G'),
Mode(A, AeolianScale).notes)
self.assertEqual(('B', 'C#', 'D', 'E', 'F#', 'G', 'A'),
Mode(B, AeolianScale).notes)
app.register_blueprint(users_blueprint)
ALLOWED_EXTENSIONS = set(['txt', 'plv', 'csv', 'mdi', 'dif'])
UPLOAD_DIR = 'uploads'
import os
app.config.from_object(os.environ['APP_SETTINGS'])
app.config['UPLOAD_FOLDER'] = UPLOAD_DIR
if not os.path.isdir(UPLOAD_DIR):
os.mkdir(UPLOAD_DIR)
# app.config['SQLALCHEMY_DATABASE_URI'] = 'postgresql://localhost/qanalyze'
defaultMode = Mode('Default', 0, 'Co', 0, 0.3, 'rockforming')
def before_request():
app.jinja_env.cache = {}
def rebal(selected, inventory):
if inventory == "cement":
db = sorted(phaselist.cementPhases)
elif inventory == "pigment":
db = sorted(phaselist.pigmentPhases)
elif inventory == "rockforming":
db = sorted(phaselist.rockPhases)
elif inventory == "chemin":
db = sorted(phaselist.cheminPhases)
def upgrade():
# -- Feed using ADIF Enumerations
# RTTY note: it should be 'ASCII' according to ADIF format but
# I think that 'RTTY' is more well-known that 'ASCII'
# CW or PSK are ASCII too, why RTTY should be named 'ASCII' ?
modes = {
"AM": ["AM"],
"FM": ["FM"],
"CW": ["CW"],
"ATV": ["ATV"],
"RTTY": ["RTTY"],
"SSTV": ["SSTV"],
"CHIP": ["CHIP64", "CHIP128"],
"CLO": ["CLO"],
"CONTESTI": ["CONTESTI"],
"DIGITALVOICE": ["DIGITALVOICE"],
"DOMINO": ["DOMINOEX", "DOMINOF"],
"DSTAR": ["DSTAR"],
"FAX": ["FAX"],
"FSK441": ["FSK441"],
"HELL": ["FMHELL", "FSKHELL", "HELL80", "HFSK", "PSKHELL"],
"ISCAT": ["ISCAT-A", "ISCAT-B"],
"JT4": ["JT4A", "JT4B", "JT4C", "JT4D", "JT4E", "JT4F", "JT4G"],
"JT6M": ["JT6M"],
"JT9": ["JT9-1", "JT9-2", "JT9-5", "JT9-10", "JT9-30"],
"JT44": ["JT44"],
"JT65": ["JT65A", "JT65B", "JT65B2", "JT65C", "JT65C2"],
"MFSK": [
"MFSK4", "MFSK8", "MFSK11", "MFSK16", "MFSK22", "MFSK31", "MFSK32",
"MFSK64", "MFSK128"
],
"MT63": ["MT63"],
"OLIVIA": [
"OLIVIA 4/125",
"OLIVIA 4/250",
"OLIVIA 8/250",
"OLIVIA 8/500",
"OLIVIA 16/500",
"OLIVIA 16/1000",
"OLIVIA 32/1000",
],
"OPERA": ["OPERA-BEACON", "OPERA-QSO"],
"PAC": ["PAC2", "PAC3", "PAC4"],
"PAX": ["PAX2"],
"PKT": ["PKT"],
"PSK": [
"FSK31",
"PSK10",
"PSK31",
"PSK63",
"PSK63F",
"PSK125",
"PSK250",
"PSK500",
"PSK1000",
"PSKAM10",
"PSKAM31",
"PSKAM50",
"PSKFEC31",
"QPSK31",
"QPSK63",
"QPSK125",
"QPSK250",
"QPSK500",
],
"PSK2K": ["PSK2K"],
"Q15": ["Q15"],
"ROS": ["ROS-EME", "ROS-HF", "ROS-MF"],
"RTTYM": ["RTTYM"],
"SSB": ["USB", "LSB"],
"THOR": ["THOR"],
"THRB": ["THRBX"],
"TOR": ["AMTORFEC", "GTOR"],
"V4": ["V4"],
"VOI": ["VOI"],
"WINMOR": ["WINMOR"],
"WSPR": ["WSPR"],
}
for mode in modes.keys():
for submode in modes[mode]:
db.session.add(Mode(mode=mode, submode=submode))
db.session.commit()
def test_invalid_mode(self):
with self.assertRaises(InvalidModeError):
Mode(C, MajorScale)
def chemin():
if request.method == 'POST':
# print request.__dict__
# Load data from request
# Ajax case
if request.is_json:
json_data = request.get_json()
data = json_data
# Regular post, text/plain encoded in body
else:
# Regular post x-www-form-urlencoded
dsample = request.form['data']
data = json.loads(dsample)
# Other type of encoding via text/plain
# a, b = request.data.split('=')
# data = json.loads(b)
sample = data['sample']
filename = sample['name']
array = sample['data']
odr_phases = data['phases']
app.logger.warning('Size of ODR array: %d', len(array))
app.logger.debug(sample)
app.logger.warning('Size of ODR phases: %d', len(odr_phases))
app.logger.warning('ODR Phases: %s', odr_phases)
# Save to file
with open(os.path.join(app.config['UPLOAD_FOLDER'], filename), 'w') as outfile:
json.dump(array, outfile)
# Initialize the session object with chemin data
session['autoremove'] = False
session['dbname'] = 'difdata_chemin.txt'
session['selected'] = phaselist.cheminPhases
session['available'] = phaselist.availablePhases
session['filename'] = filename
x = [li['x'] for li in array]
y = [li['y'] for li in array]
angle = np.asfarray(np.array(x))
diff = np.asfarray(np.array(y))
# Force mode
Lambda = 1.79027
Target = 'Co'
FWHMa = 0.0
FWHMb = 0.35
InstrParams = {"Lambda": Lambda,
"Target": Target,
"FWHMa": FWHMa,
"FWHMb": FWHMb}
# Parse phases sent by ODR
phasearray = data['phases']
selectedphases = [(d['name'], d['AMCSD_code']) for d in phasearray]
# TODO 2nd pass with selected
# Force Chemin for ODR
# Dif data captures all cristallographic data
# Load in the DB file
DBname = session['dbname']
difdata = open(DBname, 'r').readlines()
userData = (angle, diff)
# results, BG, calcdiff = qxrd.Qanalyze(userData,
# print session
results, BG, Sum, mineralpatterns = qxrd.Qanalyze(userData,
difdata,
selectedphases,
InstrParams,
session['autoremove'],
True)
# Re-create the subset of phases to select
sel, ava = rebalance(results)
session['selected'] = sel
session['available'] = ava
# print(twoT.tolist(), file=sys.stderr)
# print(userData, file=sys.stderr)
twoT = userData[0]
diff = userData[1]
angle = twoT
bgpoly = BG
xmin = min(angle)
xmax = max(angle)
# xmax = max(angle)
Imax = max(diff[min(np.where(np.array(angle) > xmin)[0]) :max(np.where(np.array(angle) > xmin)[0])])
offset = Imax / 2 * 3
offsetline = [offset] * len(angle)
difference_magnification = 1
difference = (diff - Sum) * difference_magnification
# logging.debug(results)
# logging.info("Done with processing")
offsetdiff = difference + offset
csv = 'ODR'
session['results'] = results
app.logger.warning('Length of angle array: %d', len(angle))
minerallist = [(l + BG).tolist() for l in mineralpatterns]
session['filename'] = filename
cheminMode = Mode('DefaultChemin', 0, 'Co', 0, 0, 'chemin')
template_vars = {
'phaselist': results,
'angle': angle.tolist(),
'diff': diff.tolist(),
'bgpoly': bgpoly.tolist(),
'sum': Sum.tolist(),
'difference': offsetdiff.tolist(),
'minerals': minerallist,
'url_text': csv,
'key': 'chemin',
'samplename': filename,
'mode': cheminMode,
'availablephaselist': session['available'],
'selectedphaselist': session['selected']
}
return render_template('chemin.html', **template_vars)
else:
return '''<html><body><h1>Did not get a post!</h1></body></html>'''
def chemin_process():
# Load parameters for computation
filename = session['filename']
# Extract angle, diff to populate userData
with open(os.path.join(app.config['UPLOAD_FOLDER'], filename)) as infile:
array = json.load(infile)
x = [li['x'] for li in array]
y = [li['y'] for li in array]
angle = np.asfarray(np.array(x))
diff = np.asfarray(np.array(y))
# Force mode
Lambda = 0.0
Target = 'Co'
FWHMa = 0.0
FWHMb = 0.35
InstrParams = {"Lambda": Lambda,
"Target": Target,
"FWHMa": FWHMa,
"FWHMb": FWHMb}
# Phase selection
selectedPhases = session['selected']
# Dif data captures all cristallographic data
selectedphases = []
for i in range(len(selectedPhases)):
name, code = selectedPhases[i].split('\t')
code = int(code)
selectedphases.append((name, code))
# Load in the DB file
DBname = session['dbname']
difdata = open(DBname, 'r').readlines()
userData = (angle, diff)
results, BG, Sum, mineralpatterns = qxrd.Qanalyze(userData,
difdata,
selectedphases,
InstrParams,
session['autoremove'],
True)
# Re-create the subset of phases to select
sel, ava = rebalance(results)
session['selected'] = sel
session['available'] = ava
# print(twoT.tolist(), file=sys.stderr)
# print(userData, file=sys.stderr)
twoT = userData[0]
diff = userData[1]
angle = twoT
bgpoly = BG
xmin = min(angle)
xmax = max(angle)
Imax = max(diff[min(np.where(np.array(angle) > xmin)[0])
:max(np.where(np.array(angle) > xmin)[0])])
offset = Imax / 2 * 3
offsetline = [offset] * len(angle)
difference_magnification = 1
difference = (diff - Sum) * difference_magnification
# logging.debug(results)
# logging.info("Done with processing")
offsetdiff = difference + offset
csv = 'ODR'
app.logger.warning('Length of angle array: %d', len(angle))
minerallist = [(l + BG).tolist() for l in mineralpatterns]
session['results'] = results
cheminMode = Mode('DefaultChemin', 0, 'Co', 0, 0, 'chemin')
template_vars = {
'phaselist': results,
'angle': angle.tolist(),
'diff': diff.tolist(),
'bgpoly': bgpoly.tolist(),
'sum': Sum.tolist(),
'difference': offsetdiff.tolist(),
'minerals': minerallist,
'url_text': csv,
'key': 'chemin',
'samplename': filename,
'mode': cheminMode,
'availablephaselist': session['available'],
'selectedphaselist': session['selected']
}
return render_template('chemin.html', **template_vars)
from app import db
from models import Mode
# create the database and the db table
db.create_all()
# insert data
db.session.add(Mode("default", "rock"))
db.session.add(Mode("ludo", "pigment"))
# commit the changes
db.session.commit()
