def natsort_values(df, col, inplace=False):
df = df if inplace else df.copy()
if type(col) is str:
idx = np.array(natsort.index_natsorted(df[col]))
else:
idx = np.array(natsort.index_natsorted(col))
df["__natsort_key__"] = np.argsort(idx)
df.sort_values("__natsort_key__", inplace=True)
df.drop("__natsort_key__", axis=1, inplace=True)
return df
def get_data(label, max_items):
# generate some random data
items = ['%s_%d' % (label, i + 1) for i in list(range(max_items))]
x1 = np.random.randint(low=1, high=100, size=max_items).tolist()
x2 = np.random.randint(low=1, high=100, size=max_items).tolist()
x3 = np.random.randint(low=1, high=100, size=max_items).tolist()
# insert NAs to the first row
items.insert(0, NA_ID)
x1.insert(0, NA_TEXT)
x2.insert(0, NA_TEXT)
x3.insert(0, NA_TEXT)
# create pandas dataframe
colname = '%s_pk' % label
data = {colname: items, 'x1': x1, 'x2': x2, 'x3': x3}
df = pd.DataFrame(data)
# https://stackoverflow.com/questions/29580978/naturally-sorting-pandas-dataframe
df = df.reindex(
index=order_by_index(df.index, index_natsorted(df[colname])))
# create bokeh ColumnDataSource and DataTable
columns = [
TableColumn(field=colname, title='ID'),
TableColumn(field='x1', title='x1'),
TableColumn(field='x2', title='x2'),
TableColumn(field='x3', title='x3'),
]
ds = ColumnDataSource(df)
dt = DataTable(source=ds, columns=columns, width=300, height=300)
return df, ds, dt
def test_index_natsorted_returns_integer_list_of_sort_order_for_input_list():
a = ['num3', 'num5', 'num2']
b = ['foo', 'bar', 'baz']
index = index_natsorted(a)
assert index == [2, 0, 1]
assert [a[i] for i in index] == ['num2', 'num3', 'num5']
assert [b[i] for i in index] == ['baz', 'foo', 'bar']
def buscar(busqueda, categoria):
"""
docstring
"""
if not busqueda == "":
todos_los_productos = []
driver.get(mercados.select_market + busqueda)
producto_a_objeto(todos_los_productos)
df = pd.DataFrame(todos_los_productos)
orden = "producto"
ordenado = df.sort_values(
by=str(orden),
key=lambda x: np.argsort(index_natsorted(df[str(orden)])))
today = str(datetime.date.today())
localdir = os.getcwd()
#time = str(datetime.datetime.now()).replace(" ", "_").replace(":", "-")
if not os.path.isdir(localdir + "/tablas/select_market/" + today):
os.mkdir(localdir + "/tablas/select_market/" + today)
if not os.path.isfile(
f"tablas/select_market/{today}/por_{orden}_{categoria}_tabla.csv"
):
f = open(
f"tablas/select_market/{today}/por_{orden}_{categoria}_tabla.csv",
"x")
f.write(ordenado.to_csv(index=False))
f.close()
busqueda = ""
orden = ""
print("busqueda finalizada")
def test_index_natsorted_returns_integer_list_of_sort_order_for_input_list():
given = ["num3", "num5", "num2"]
other = ["foo", "bar", "baz"]
index = index_natsorted(given)
assert index == [2, 0, 1]
assert [given[i] for i in index] == ["num2", "num3", "num5"]
assert [other[i] for i in index] == ["baz", "foo", "bar"]
def prepare(df):
# Sort columns
df = df.sort_index(axis=1)
# Natsort all rows
df = df.reindex(index=order_by_index(df.index, index_natsorted(zip(df.to_numpy()))))
# Recreate index for comparison later
return df
def test_index_natsorted_returns_integer_list_of_sort_order_for_input_list():
a = ['num3', 'num5', 'num2']
b = ['foo', 'bar', 'baz']
index = index_natsorted(a)
assert index == [2, 0, 1]
assert [a[i] for i in index] == ['num2', 'num3', 'num5']
assert [b[i] for i in index] == ['baz', 'foo', 'bar']
def test_index_natsorted_returns_integer_list_of_sort_order_for_input_list():
given = ["num3", "num5", "num2"]
other = ["foo", "bar", "baz"]
index = index_natsorted(given)
assert index == [2, 0, 1]
assert [given[i] for i in index] == ["num2", "num3", "num5"]
assert [other[i] for i in index] == ["baz", "foo", "bar"]
def test_index_natsorted_returns_integer_list_of_sort_order_for_input_list():
a = ["num3", "num5", "num2"]
b = ["foo", "bar", "baz"]
index = index_natsorted(a)
assert index == [2, 0, 1]
assert [a[i] for i in index] == ["num2", "num3", "num5"]
assert [b[i] for i in index] == ["baz", "foo", "bar"]
def prepare(self, df):
# Sort columns
df = df.sort_index(axis=1)
# Natsort all rows
df = df.reindex(index=order_by_index(df.index, index_natsorted(zip(df.to_numpy()))))
# Recreate index for comparison later
df.reset_index(level=0, drop=True, inplace=True)
return df
def test_index_natsorted():
# Return the indexes of how the iterable would be sorted.
a = ['num3', 'num5', 'num2']
b = ['foo', 'bar', 'baz']
index = index_natsorted(a)
assert index == [2, 0, 1]
assert [a[i] for i in index] == ['num2', 'num3', 'num5']
assert [b[i] for i in index] == ['baz', 'foo', 'bar']
# It accepts a key argument.
c = [('a', 'num3'), ('b', 'num5'), ('c', 'num2')]
assert index_natsorted(c, key=itemgetter(1)) == [2, 0, 1]
# It can avoid "unorderable types" on Python 3
a = [46, '5a5b2', 'af5', '5a5-4']
assert index_natsorted(a) == [3, 1, 0, 2]
def _nat_order_labels(self, mat, labels):
# get the natural order indices
natindices = index_natsorted(labels)
# order the matrix
ordered_mat = np.array(order_by_index(mat, natindices))
ordered_labels = np.array(order_by_index(labels, natindices))
return ordered_mat, ordered_labels
def natural_sort(df, by='id', index=False):
'''
Sort a pandas dataframe "naturally" by column or by index.
'''
if index:
return df.reindex(index=natsorted(df.index))
return df.reindex(index=order_by_index(df.index, index_natsorted(df[by])))
def bar_plot_mmgbsa_results(excel_file, sort=True, titles=None):
"""
Load data from an Excel file with the summary of the MMGBSA results, in a sheet which has to be called "MMGBSA".
Create a plot for each ligand that is found under the 'Ligand' column in the table.
:param excel_file: str, Name of the Excel file with the data
:param sort: bool, Whether to sort the plot by increasing MMGBSA values
:param titles: list, Name for each of the plots (as many as there are ligands in the table)
:return f_list: list, A list of matplotlib figures
"""
# sns.set_style('whitegrid')
df = pd.read_excel(excel_file, sheetname="MMGBSA")
df = df.reindex(index=order_by_index(df.index, index_natsorted(df.Run)))
ligands = df.Ligand.unique()
f_list = []
if titles is None:
titles = [None for _ in ligands]
elif len(titles) != len(ligands):
raise ValueError('len of ligands and titles is not equal.')
for lig, title in zip(ligands, titles):
lig_df = df[df.Ligand == lig]
if sort:
lig_df.sort_values(by='MMGBSA (mean)', inplace=True)
ax = lig_df.plot(x="Run", y="MMGBSA (mean)", yerr='MMGBSA (Std)', kind='bar',
legend=False, figsize=figure_dims(1400), title=title)
overall_mean = lig_df['MMGBSA (mean)'].mean()
overall_std = lig_df['MMGBSA (mean)'].std()
print("{} {:02f} {:02f}".format(lig, overall_mean, overall_std))
xmin, xmax = ax.get_xlim()
# Mean line
ax.plot(
[xmin, xmax], [overall_mean, overall_mean],
linewidth=1.5,
color='blue'
)
# Upper std bar
ax.plot(
[xmin, xmax],
[overall_mean + overall_std, overall_mean + overall_std],
linestyle='dashed',
linewidth=1,
color='blue'
)
# Lower std bar
ax.plot(
[xmin, xmax],
[overall_mean - overall_std, overall_mean - overall_std],
linestyle='dashed',
linewidth=1,
color='blue'
)
ax.set_ylim(top=0)
ax.set_ylabel(ylabel=r'$\Delta$G binding (kcal/mol)', size=14)
ax.set_xlabel(xlabel='Run', size=14)
f = pp.gcf()
f.tight_layout()
f_list.append(f)
return f_list
def __order_feats(self, feats_path, feats):
video_name = feats_path.split('/')[-1]
video_name = utils.remove_extension(video_name)
frames_names = self.__annotation_dict[video_name]
idx = natsort.index_natsorted(frames_names)
feats = feats[idx]
return feats
def sort(self, column, order):
self.layoutAboutToBeChanged.emit()
if order == 0:
self._dataframe = self._dataframe.reindex(index=order_by_index(
self._dataframe.index,
index_natsorted(
eval('self._dataframe.%s' %
(list(self._dataframe.columns)[column])))))
else:
self._dataframe = self._dataframe.reindex(index=order_by_index(
self._dataframe.index,
reversed(
index_natsorted(
eval('self._dataframe.%s' %
(list(self._dataframe.columns)[column]))))))
self._dataframe.reset_index(inplace=True, drop=True)
self.setDataFrame(self._dataframe)
self.layoutChanged.emit()
def avgPrefs(prefsfiles):
"""Gets average of site-specific preferences.
Args:
`prefsfiles` (list)
List of CSV files containing preferences, must all be
for same sites and characters.
Returns:
A `pandas.DataFrame` containing the average of the
preferences in `prefsfiles`. In this returned
data frame, `site` is the index
>>> tf1 = tempfile.NamedTemporaryFile
>>> tf2 = tempfile.NamedTemporaryFile
>>> with tf1(mode='w') as file1, tf2(mode='w') as file2:
... x = file1.write('site,A,C,G,T\\n'
... '10,0.2,0.2,0.5,0.1\\n'
... '2a,0.3,0.3,0.3,0.1')
... file1.flush()
... x = file2.write('site,A,C,G,T\\n'
... '10,0.4,0.1,0.1,0.4\\n'
... '2a,0.3,0.4,0.1,0.2')
... file2.flush()
... avg = avgPrefs([file1.name, file2.name])
>>> (avg['site'] == ['2a', '10']).all()
True
>>> numpy.allclose(avg['A'], [0.3, 0.3])
True
>>> numpy.allclose(avg['C'], [0.35, 0.15])
True
>>> numpy.allclose(avg['G'], [0.2, 0.3])
True
>>> numpy.allclose(avg['T'], [0.15, 0.25])
True
"""
assert len(prefsfiles) >= 1
prefs = [
pandas.read_csv(f, index_col='site').sort_index() for f in prefsfiles
]
# make sure all have the same columns in the same order
cols = prefs[0].columns
for i in range(len(prefs)):
assert set(cols) == set(prefs[i].columns)
prefs[i] = prefs[i][cols]
avgprefs = pandas.concat(prefs).groupby('site').mean().reset_index()
# natural sort by site: https://stackoverflow.com/a/29582718
avgprefs = avgprefs.reindex(index=natsort.order_by_index(
avgprefs.index, natsort.index_natsorted(avgprefs.site, signed=True)))
return avgprefs
def natsort_values(df, cols, ascending=True):
"""Substitute for pd.DataFrame.sort_values
"""
from natsort import index_natsorted
if not isinstance(cols, list):
cols = [cols]
values = np.array([np.argsort(index_natsorted(df[c])) for c in cols]).T
ix = (pd.DataFrame(values, columns=cols)
.sort_values(cols, ascending=ascending)
.index)
return df.iloc[list(ix)].copy()
def rebuild_dataframes(self, metabolite):
"""
Function to assemble datas after calculations into final dataframe
with a natural sort on index level "sources"
:param metabolite: metabolite to process
:type metabolite: str
:return data_df: dataframe ccntaining calculated concentrations
:rtype: class: 'Pandas.Dataframe'
:return cal_df: dataframe containing data used for calibration curves
:rtype cal_df: class: 'Pandas.Dataframe'
"""
self._logger.debug("Rebuilding dataframes\n")
data_df = pd.DataFrame.from_dict({
"sources":
self.tmp_sample_dict["sources"],
"Linear Concentrations (µM)":
self.tmp_sample_dict["Linear result"],
"Quadratic Concentrations (µM)":
self.tmp_sample_dict["Quadratic result"]
})
cal_df = pd.DataFrame.from_dict(self.tmp_cal_dict)
# We sort values naturally by sources before putting in dfs
data_df = data_df.sort_values(
by="sources", key=lambda x: np.argsort(index_natsorted(x)))
cal_df = cal_df.sort_values(
by="sources", key=lambda x: np.argsort(index_natsorted(x)))
# We need to insert the metabolite name before returning the dfs
data_df = data_df.assign(metabolite=metabolite)
cal_df = cal_df.assign(metabolite=metabolite)
data_df.set_index(['metabolite', 'sources'], inplace=True)
cal_df.set_index(['metabolite', 'sources'], inplace=True)
return data_df, cal_df
def test_index_natsorted():
# Return the indexes of how the iterable would be sorted.
a = ['num3', 'num5', 'num2']
b = ['foo', 'bar', 'baz']
index = index_natsorted(a)
assert index == [2, 0, 1]
assert [a[i] for i in index] == ['num2', 'num3', 'num5']
assert [b[i] for i in index] == ['baz', 'foo', 'bar']
assert index_natsorted(a, reverse=True) == [1, 0, 2]
# It accepts a key argument.
c = [('a', 'num3'), ('b', 'num5'), ('c', 'num2')]
assert index_natsorted(c, key=itemgetter(1)) == [2, 0, 1]
# It can avoid "unorderable types" on Python 3
a = [46, '5a5b2', 'af5', '5a5-4']
assert index_natsorted(a) == [3, 1, 0, 2]
# It can sort lists of lists.
data = [['a1', 'a5'], ['a1', 'a40'], ['a10', 'a1'], ['a2', 'a5']]
assert index_natsorted(data) == [0, 1, 3, 2]
# It can sort paths too
a = ['/p/Folder (10)/',
'/p/Folder/',
'/p/Folder (1)/']
assert index_natsorted(a, alg=ns.PATH) == [1, 2, 0]
def _get1d_neighbors(self, electrodechans, chanlabel):
# naturally sort the gridlayout
natinds = index_natsorted(electrodechans)
sortedelec = electrodechans[natinds]
# get the channel index - ijth index
chanindex = sortedelec.index(chanlabel)
# get the neighboring indices and channels
nbrinds = [chanindex + 1, chanindex - 1]
nbrchans = [chanlabel[ind] for ind in nbrinds]
return nbrchans, nbrinds
def test_index_versorted():
a = ['1.9.9a', '1.11', '1.9.9b', '1.11.4', '1.10.1']
assert index_versorted(a) == index_natsorted(a, alg=ns.VERSION)
assert index_versorted(a, reverse=True) == index_versorted(a)[::-1]
a = [('a', '1.9.9a'), ('a', '1.11'), ('a', '1.9.9b'),
('a', '1.11.4'), ('a', '1.10.1')]
assert index_versorted(a) == [0, 2, 4, 1, 3]
# It can sort paths too
a = ['/p/Folder (10)/file1.1.0.tar.gz',
'/p/Folder/file1.1.0.tar.gz',
'/p/Folder (1)/file1.1.0 (1).tar.gz',
'/p/Folder (1)/file1.1.0.tar.gz']
assert index_versorted(a, alg=ns.PATH) == [1, 3, 2, 0]
def main():
"""Main function for pyim-annotate."""
args = parse_args()
insertions = Insertion.from_csv(args.insertions, sep='\t')
annotator = args.caller.from_args(args)
annotated = list(annotator.annotate(insertions))
annotated_frame = Insertion.to_frame(annotated)
annotated_frame = annotated_frame.reindex(index=order_by_index(
annotated_frame.index, index_natsorted(annotated_frame.id)))
annotated_frame.to_csv(str(args.output), sep='\t', index=False)
def checkdf(self, p, x):
"""
:return: merged dataframes
"""
labels = x.keys()
colnames = ['standard_hue', 'ntrial', 'all_intensities', 'all_responses', 'reversal value']
df = pd.DataFrame(columns=colnames, index=labels)
for label in labels:
sheet = x[label]
df.loc[label, colnames[0]] = float(p[p['label'] == label]['standard'])
df.loc[label, colnames[1]] = len(sheet)
df.loc[label, colnames[2]] = np.array((sheet['All Intensities']))
df.loc[label, colnames[3]] = np.array((sheet['All Responses']))
df.loc[label, colnames[4]] = np.array((sheet['Reversal Intensities']))
df = df.reindex(index=order_by_index(df.index, index_natsorted(df.index, reverse=False)))
return df
def sumxrl(self):
par, xls, count = self.readxrl()
dfs = pd.concat([self.checkdf(p, x) for p, x in zip(par, xls)], axis=0)
summary = dfs.groupby(level=0).agg({
'standard_hue':
'unique',
'ntrial':
lambda x: sum(x) / count,
'reversal value': [self.meanvalue, self.stdvalue],
'all_responses': [self.meanvalue, self.stdvalue]
})
summary = summary.reindex(index=order_by_index(
summary.index, index_natsorted(summary.index, reverse=False)))
return dfs, summary
def takeMinLineMmap(linesList, outputFile, mapping, writePos, actualFilePos,
mapSize, rFileSize):
"""
Writes the smallest line from linesList to outputFile using the
mapped approach.
"""
minRow = natsort.index_natsorted(linesList, key=lambda x: (x is None, x))
bufferListIndex = int(minRow[0])
minLine = natsort.natsorted(linesList, key=lambda x: (x is None, x))
minBytes = bytes(minLine[0][1], 'utf-8')
mapping, writePos, actualFilePos = writeln_mmap(mapping, writePos,
actualFilePos, mapSize,
rFileSize, outputFile,
minBytes)
linesList[bufferListIndex] = [None, None]
return bufferListIndex, mapping, writePos, actualFilePos
def _get_stranded_f(self, half_entries, f, sort=False):
counter = 0
dfs = []
chromosomes = self.chromosomes
if f == "tail":
chromosomes = reversed(chromosomes)
default = pd.DataFrame(columns=self.columns)
for chromosome in chromosomes:
plus = self.dfs.get((chromosome, "+"), default)
minus = self.dfs.get((chromosome, "-"), default)
if sort:
plus = plus.sort_values(sort_cols)
minus = minus.sort_values(sort_cols)
plus = getattr(plus, f)(half_entries)
minus = getattr(minus, f)(half_entries)
df = pd.concat([plus, minus])
if sort:
df = df.sort_values(sort_cols)
counter += len(df)
dfs.append(df)
if counter >= half_entries:
break
df = pd.concat(dfs)
# got twice as many entries as needed before sort. Halve here:
df = getattr(df, f)(half_entries)
# dfs = {df.Chromosome.iloc[0]: df for df in}
df = df.reset_index(drop=True)
df = df.reindex(index=natsort.order_by_index(
df.index, natsort.index_natsorted(zip(df.Chromosome))))
return df
def main(options):
# open all files
# read all headers
fnames = options.inbw
bw = {}
header = {}
chroms = {}
for fname in fnames:
print("opening file for input: " + os.path.split(fname)[1])
bw[fname] = pyBigWig.open(fname)
header[fname] = bw[fname].chroms()
chroms[fname] = list(header[fname].keys())[0]
# define order based on chromosome names extracted from headers
idx = natsort.index_natsorted(chroms)
fnames = natsort.order_by_index(fnames, idx)
# open bigwig for output
print("opening bigwig file for output (%s)" % options.outfname)
out_bw = pyBigWig.open(options.outfname, "w")
assert (out_bw is not None)
# construct sorted header and write to output
header = [list(header[f].items())[0] for f in fnames]
print(str(header))
out_bw.addHeader(header)
# loop over sorted chromosome-names/file-names
## import data from input bw
## add read data to output bw
for fname in fnames:
print("exporting data from chrom; " + chroms[fname] + " (file: " +
fname + ")")
ints = bw[fname].intervals(chroms[fname])
chrs = [chroms[fname]] * len(ints)
out_bw.addEntries(chrs, [i[0] for i in ints],
ends=[i[1] for i in ints],
values=[i[2] for i in ints])
print("closing bigwig file for output (%s)" % options.outfname)
out_bw.close()
return True
def summary_table(table):
# generate summary by adding all values by piovote table
summary = table.pivot_table(values=ps.DOSE_MSV,
index=[ps.POINT_NAME, ps.OCCUPANCY_FACTOR],
aggfunc=sum)
# get sort order, natsorted gives 0,1,2,3,4,5,6,7,8,8, 10 instead of
# 0, 1, 10,2, 20 etc.
new_index = index_natsorted(summary.index)
# sort table by point name
summary = summary.iloc[new_index]
summary.reset_index(inplace=True)
# add corrected dose for occupancy
summary[ps.DOSE_OCCUPANCY_MSV] = summary[ps.DOSE_MSV] * \
summary[ps.OCCUPANCY_FACTOR]
return summary
def convert_clusters(clusters, cluster_size_min, cluster_size_max, out_path, normalise):
'''
Args:
clusters(Object): Clusters object
cluster_size_min(int): minimum size of cluster (more than or equal to int)
cluster_size_max(int): maximum size of cluster (less than or equal to int)
out_path(str): Out file path
'''
assert cluster_size_min > 1, 'Minimum cluster size needs to be > 1'
all_clusters = []
for barcode, cluster in clusters.get_items():
cs = cluster.size('DPM')
if cs >= cluster_size_min and cs <= cluster_size_max:
all_clusters.extend(cluster2sfws(cluster, 'DPM', normalise))
column_names=['str1', 'chr1', 'pos1', 'frag1', 'str2', 'chr2', 'pos2','frag2', 'score']
df = pd.DataFrame(all_clusters, columns=column_names)
df_out = df.reindex(index=order_by_index(df.index, index_natsorted(zip(df.chr1, df.chr2, df.pos1, df.pos2))))
df_out.to_csv(out_path, sep=' ', index=False, header=False)
def natsort_contacts(self) -> Tuple:
"""
Naturally sort the contacts.
Keeps the applied indices in self.naturalinds
Returns
-------
naturalinds
"""
if self.naturalinds == None:
self.naturalinds = index_natsorted(self.chanlabels)
self.chanlabels = np.array(
order_by_index(self.chanlabels, self.naturalinds))
else:
warnings.warn(
"Already naturally sorted contacts! Extract channel labels naturally sorted by calling "
"chanlabels, and apply ordering to other channel level data with naturalinds."
)
return self.naturalinds
def write_click_csv(self, n_frames):
out = pd.DataFrame(self.mouse_clicks)
out = out.reindex(index=order_by_index(
out.index, index_natsorted(out['frame'], reverse=False)))
out = out.assign(time=[0]*out.shape[0])
out = out.assign(visible=[1]*out.shape[0])
cols = ['frame', 'time', 'visible', 'x', 'y']
out = out[cols]
# reindex or change the order of columns
str_ = out.to_csv(sep=';', index=False)
h, w = self.frames[0].shape[:2]
header = 'VideoWidth:{}\nVideoHeight:{}\nDisplayWidth:0\nDisplayHeight:0\n'.format(w, h)
str_ = header + str_
text_file = open(self.out_csv, 'w')
n = text_file.write(str_)
text_file.close()
print('written {}'.format(self.out_csv))
def list_of_names(fname='SavedData/searchResult.php'):
names = []
ulist = []
bs = BeautifulSoup(open(fname), features='lxml')
pbar = ProgressBar()
for species in pbar(bs.findAll('i')):
for parents in species.parents:
if parents.name == 'td':
[names.append(name) for name in species.contents]
[ulist.append(x) for x in names
if x not in ulist] # deleting double values
df = pd.DataFrame() # create dataframe
df['name'] = ulist
df = df.reindex(index=order_by_index(
df.index, index_natsorted(df['name'],
reverse=False))) # sort alphabetically
df = df.reset_index(drop=True) # fix index
return df
def test_index_natsorted_returns_reversed_integer_list_of_sort_order_for_input_list_with_reverse_option():
a = ['num3', 'num5', 'num2']
assert index_natsorted(a, reverse=True) == [1, 0, 2]
else "\\newline" if len(x) <= 1
else x[0],
x[1:].strip()) for x in
lines[footnotes_start:]])
postbl = Table([Column(data=names, name='Source Name'),
Column(data=coords.ra.to_string(unit=u.hour, sep=':', precision=2), name='RA'),
Column(data=coords.dec.to_string(unit=u.deg, sep=':', precision=1), name='Dec'),
Column(data=radii, name='Radius'),
Column(data=(radii*5.1*u.kpc).to(u.pc, u.dimensionless_angles()), name='Phys. Radius'),
SEDclasscolumn,
classificationcolumn,
])
import natsort
postbl = postbl[natsort.index_natsorted(postbl['Source Name'])]
latexdict['header_start'] = '\label{tab:positions}'
latexdict['caption'] = 'Source Positions'
latexdict['tablefoot'] = ('\par\nObjects with name e\#d are the diffuse '
'counterparts to point sources. '
'The absolute positional accuracy is '
'$\sim0.2\\arcsec$. '
'Sources with no radius are unresolved, '
'with '
'upper limits of 0.3\\arcsec (0.007 pc).'
'Source names correspond to the labels in Figures '
'\\ref{fig:coverview_pointsrcs} and '
'\\ref{fig:coverview_diffuse}.'
'\\\\\n' +
footer)
def test_index_versorted_returns_results_identical_to_index_natsorted():
a = ["1.9.9a", "1.11", "1.9.9b", "1.11.4", "1.10.1"]
# index_versorted is retained for backwards compatibility
assert index_versorted(a) == index_natsorted(a)
def prof_str_index_key(a):
print('*** Basic Index Call With Key ***')
for _ in py23_range(1000):
index_natsorted(a, key=lambda x: x.upper())
def test_index_humansorted_returns_results_identical_to_index_natsorted_with_LOCALE():
a = ['Apple', 'corn', 'Corn', 'Banana', 'apple', 'banana']
assert index_humansorted(a) == index_natsorted(a, alg=ns.LOCALE)
def test_index_versorted_returns_results_identical_to_index_natsorted():
a = ['1.9.9a', '1.11', '1.9.9b', '1.11.4', '1.10.1']
# index_versorted is retained for backwards compatibility
assert index_versorted(a) == index_natsorted(a)
def test_index_natsorted_returns_integer_list_of_nested_input_list():
data = [['a1', 'a5'], ['a1', 'a40'], ['a10', 'a1'], ['a2', 'a5']]
assert index_natsorted(data) == [0, 1, 3, 2]
def test_index_realsorted_is_identical_to_index_natsorted_with_real_alg(float_list):
assert index_realsorted(float_list) == index_natsorted(float_list, alg=ns.REAL)
def test_index_realsorted_returns_results_identical_to_index_natsorted_with_REAL():
a = ["a50", "a51.", "a50.31", "a-50", "a50.4", "a5.034e1", "a50.300"]
assert index_realsorted(a) == index_natsorted(a, alg=ns.REAL)
def test_index_humansorted_returns_results_identical_to_index_natsorted_with_LOCALE():
a = ["Apple", "corn", "Corn", "Banana", "apple", "banana"]
assert index_humansorted(a) == index_natsorted(a, alg=ns.LOCALE)
def test_index_natsorted_applies_key_function_before_sorting():
c = [("a", "num3"), ("b", "num5"), ("c", "num2")]
assert index_natsorted(c, key=itemgetter(1)) == [2, 0, 1]
def test_index_natsorted_handles_unorderable_types_error_on_Python3():
a = [46, "5a5b2", "af5", "5a5-4"]
assert index_natsorted(a) == [3, 1, 0, 2]
from astropy.table import Table, Column
from astropy import units as u
from latex_info import latexdict, format_float, round_to_n, strip_trailing_zeros
import natsort
tbl = Table.read('core_continuum_and_line.ipac', format='ascii.ipac')
inds = natsort.index_natsorted(tbl['SourceID'])
tbl = tbl[inds]
tbl_towrite = tbl['SourceID', 'RA', 'Dec', 'cont_flux0p2arcsec',
'cont_flux0p4arcsec',
#'BrightestFittedPeakPixBrightness',
'BrightestFittedPeakPixBrightnessWithcont',
'T_corrected_0p2aperturemass',
'T_corrected_peakmass',
'Categories',
#'Classification',
]
for row in tbl_towrite:
if '_' in row['SourceID']:
row['SourceID'] = row['SourceID'].replace("_"," ")
new_names = {'SourceID': 'Source ID',
'cont_flux0p2arcsec': '$S_{\\nu}(0.2\\arcsec)$',
'cont_flux0p4arcsec': '$S_{\\nu}(0.4\\arcsec)$',
#'BrightestFittedPeakPixBrightness': '$T_{B,max}(\mathrm{line})$',
'BrightestFittedPeakPixBrightnessWithcont': '$T_{B,max}$',#(\mathrm{line+cont})$',
'T_corrected_0p2aperturemass': 'M$(T_B, 0.2\\arcsec)$',
def prof_str_index(a):
print('*** Basic Index Call ***')
for _ in py23_range(1000):
index_natsorted(a)
def test_index_natsorted_applies_key_function_before_sorting():
c = [('a', 'num3'), ('b', 'num5'), ('c', 'num2')]
assert index_natsorted(c, key=itemgetter(1)) == [2, 0, 1]
def test_index_natsorted_handles_unorderable_types_error_on_Python3():
a = [46, '5a5b2', 'af5', '5a5-4']
assert index_natsorted(a) == [3, 1, 0, 2]
def control_timetable(timetable, header):
print(Fore.YELLOW + '{:-^30}'.format(header))
start_order_details = []
for i in range(1, 4):
start_order_details.append([j[1] for j in timetable if j[0] == i])
# разбиваем интервалы по деталям, выйдет 4 списка, использ.
# для подсчета ожидания
order_by_details = []
for i in start_order_details[0]:
order_by_details.append([j for j in timetable if j[1] == i])
# для подсчета простоев сорт. наше расписание по ГВМ
timetable = ordered_timetable(timetable)
# список порядка запуска деталей на ГВМ, убираем номер операции
# и ГВМ со списка интервалов, для обсчета ожидания
start_order_gvm = []
order_by_details_norm = []
for i in order_by_details:
start_order_gvm.append([j[:1][0] for j in i])
order_by_details_norm.append([j[2:] for j in i])
# считаем послеоперационные простои ГВМ
timetable = downtime(timetable)
for i in range(3):
index = natsort.index_natsorted(start_order_details[i])
timetable[i] = natsort.order_by_index(timetable[i], index)
print(Fore.WHITE + "\nDowntime: " + Fore.CYAN +
'{}'.format(min([sum(i) for i in timetable])))
for i in timetable:
print(Fore.WHITE + '{!s:>18s}'.format(i))
# считаем ожидание деталей перед обработкой
print("\nWaiting:")
order_by_details = waiting(order_by_details_norm)
# упорядочиваем ожидание для каждой детали по ГВМ: 1 2 3
index = natsort.index_natsorted(start_order_details[0])
order_by_details = natsort.order_by_index(order_by_details, index)
start_order_gvm = natsort.order_by_index(start_order_gvm, index)
for i in range(4):
index = natsort.index_natsorted(start_order_gvm[i])
order_by_details[i] = natsort.order_by_index(order_by_details[i],
index)
for i in order_by_details:
print(Fore.WHITE + '{!s:>16s}'.format(i))
#считаем локальний резерв
order_by_details = numpy.transpose(order_by_details)
print('\nLocal resource:\n')
for i in range(3):
for j in range(4):
first = timetable[i][j]
try:
second = order_by_details[i+1][j]
except IndexError:
second = float('inf')
print(" L({0}, {1}) = min({2}, {3}) = {4}".format( \
i+1, j+1, first, second, min(first, second)))
print('\n')
print(Style.RESET_ALL)
def test_index_natsorted_returns_integer_list_in_proper_order_for_input_paths_with_PATH():
a = ['/p/Folder (10)/',
'/p/Folder/',
'/p/Folder (1)/']
assert index_natsorted(a, alg=ns.PATH) == [1, 2, 0]
def test_index_natsorted_returns_integer_list_of_nested_input_list():
data = [["a1", "a5"], ["a1", "a40"], ["a10", "a1"], ["a2", "a5"]]
assert index_natsorted(data) == [0, 1, 3, 2]
def test_index_realsorted_returns_results_identical_to_index_natsorted_with_REAL():
a = ['a50', 'a51.', 'a50.31', 'a-50', 'a50.4', 'a5.034e1', 'a50.300']
assert index_realsorted(a) == index_natsorted(a, alg=ns.REAL)
def test_index_natsorted_reverse():
given = ["num3", "num5", "num2"]
assert index_natsorted(given, reverse=True) == index_natsorted(given)[::-1]
nirassociations = {x[:split1].strip():x[split2:split3].strip() for x in lines[1:]}
goldaderassociations = {x[:split1].strip():x[split3:].strip() for x in lines[1:]}
names = sorted(xrayassociations.keys())
keep = [name for name in names if not (xrayassociations[name]=='-' and nirassociations=='-')]
xrayassociations_column = Column(data=[xrayassociations[x] for x in keep],
name="X-ray")
nirassociations_column = Column(data=[nirassociations[x] for x in keep],
name="NIR")
goldaderassociations_column = Column(data=[goldaderassociations[x] for x in keep],
name="Goldader 1994")
names_column = Column(data=keep, name='Source Name')
tbl = Table([names_column, xrayassociations_column, nirassociations_column,
goldaderassociations_column])
OK = (tbl['X-ray'] != '-') | (tbl['NIR'] != '-') | (tbl['Goldader 1994'] != '-')
tbl=tbl[OK]
import natsort
tbl = tbl[natsort.index_natsorted(tbl['Source Name'])]
latexdict['header_start'] = '\label{tab:associations}'
latexdict['caption'] = 'Source Associations'
latexdict['tablefoot'] = ('')
latexdict['col_align'] = 'l'*len(tbl.colnames)
#latexdict['tabletype'] = 'longtable'
#latexdict['tabulartype'] = 'longtable'
tbl.write(paths.tpath('associations.tex'), format='ascii.latex',
latexdict=latexdict, formats={},)
import numpy as np
from astropy.table import Table
import paths
from latex_info import latexdict, exp_to_tex, format_float
import natsort
tbl = Table.read("../tables/obs_meta.tbl", format="ascii", delimiter="|")
tbl = tbl[natsort.index_natsorted(tbl["Date"])]
latexdict["header_start"] = "\label{tab:obs_meta}"
latexdict["caption"] = "Observation Metadata"
latexdict["tablefoot"] = ""
latexdict["col_align"] = "l" * 8
# latexdict['tabletype'] = 'longtable'
# latexdict['tabulartype'] = 'longtable'
tbl.write(paths.tpath("obs_meta.tex"), format="ascii.latex", latexdict=latexdict, formats={}, overwrite=True)
data,error = zip(*dataerror)
#data = [sp.specfit.parinfo[ii].value
# for sp in spectra]
#error = [sp.specfit.parinfo[ii].error
# for sp in spectra]
column = table.Column(data=data,
name='H77a_'+parname,
unit=unit)
tbl.add_column(column)
column = table.Column(data=error,
name='eH77a_'+parname,
unit=unit)
tbl.add_column(column)
# sort such that e10 comes after e9
tbl = tbl[natsort.index_natsorted(tbl['ObjectName'])]
detection_note = ['-' if name in detections else
'weak' if name in weakdetections else
'none'
for name in tbl['ObjectName']]
tbl.add_column(table.Column(data=detection_note, name='DetectionStatus'))
ok = np.array([row['ObjectName'] in detections+weakdetections
for row in tbl])
tbl[ok].write(paths.tpath('H77a_spectral_fits.ipac'), format='ascii.ipac')
for old,new in [('ObjectName','Object Name'),
('H77a_amplitude', 'Amplitude',),
('eH77a_amplitude','$E$(Amplitude)',),
def test_index_natsorted_applies_key_function_before_sorting():
given = [("a", "num3"), ("b", "num5"), ("c", "num2")]
expected = [2, 0, 1]
assert index_natsorted(given, key=itemgetter(1)) == expected
def test_index_versorted_returns_results_identical_to_index_natsorted_with_VERSION():
a = ['1.9.9a', '1.11', '1.9.9b', '1.11.4', '1.10.1']
assert index_versorted(a) == index_natsorted(a, alg=ns.VERSION)
+ list(
(rounded(thisspec.specfit.parinfo.AMPLITUDE0.value, thisspec.specfit.parinfo.AMPLITUDE0.error) * u.Jy).to(
u.mJy
)
)
+ list(rounded(thisspec.specfit.parinfo.SHIFT0.value, thisspec.specfit.parinfo.SHIFT0.error) * u.km / u.s)
+ list(rounded(thisspec.specfit.parinfo.WIDTH0.value, thisspec.specfit.parinfo.WIDTH0.error) * u.km / u.s)
+ [np.round(r_eff, 1) * u.arcsec]
# [np.round(thisspec.header['APAREA']*(np.pi/180.)**2, int(np.ceil(-np.log10(thisspec.header['APAREA']*(np.pi/180.)**2)))+1)*u.sr]
)
# sort such that e10 comes after e9
import natsort
tbl = tbl[natsort.index_natsorted(tbl["Object Name"])]
detection_note = [
"-" if name in detections else "ambig" if name in ambiguousdetections else "none" for name in tbl["Object Name"]
]
tbl.add_column(table.Column(data=detection_note, name="Detection Status"))
ok = np.array([row["Object Name"] in detections + ambiguousdetections for row in tbl])
tbl[ok].write(paths.tpath("H2CO22_hiiregion_spectral_fits.ecsv"), format="ascii.ecsv")
for row in tbl:
if "_" in row["Object Name"]:
row["Object Name"] = row["Object Name"].replace("_", "\_")
latexdict["header_start"] = "\label{tab:absorption22}"