def single_file_item_iterator(
f_csv,
config=None,
section='parse',
progress_bar=False,
text_column=None,
include_filename=True,
):
'''
Iterates over a single file
'''
if config is None:
config = simple_config.load()
config = simple_config.load()
# Make sure the file we requested exists
assert(f_csv in get_section_filenames(section))
INPUT_ITR = CSV_database_iterator(
[f_csv],
config["target_column"],
progress_bar=progress_bar,
include_filename=include_filename,
)
for row in INPUT_ITR:
if text_column is not None:
row['text'] = row[text_column]
yield row
def load_document_vectors():
config_score = simple_config.load()["score"]
config_MC = simple_config.load()["metacluster"]
score_method = config_MC['score_method']
f_h5 = os.path.join(
config_score["output_data_directory"],
config_score['document_scores']["f_db"],
)
with h5py.File(f_h5, 'r') as h5:
g = h5[score_method]
# Load the _refs
_refs = g["_ref"][:]
# Require the _refs to be in order as a sanity check
if not (np.sort(_refs) == _refs).all():
msg = "WARNING, data out of sort order from _refs"
raise ValueError(msg)
docv = g["V"][:]
return {"docv": docv, "_refs": _refs}
def load_document_vectors():
config_score = simple_config.load("score")
config_MC = simple_config.load("metacluster")
score_method = config_MC['score_method']
text_column = config_MC['score_column']
f_h5 = os.path.join(
config_score["output_data_directory"],
config_score['document_scores']["f_db"],
)
with h5py.File(f_h5,'r') as h5:
g = h5[score_method][text_column]
corpus_keys = g.keys()
# Load the _refs
_refs = np.hstack([g[key]["_ref"][:] for key in corpus_keys])
# Require the _refs to be in order as a sanity check
if not (np.sort(_refs) == _refs).all():
msg = "WARNING, data out of sort order from _refs"
raise ValueError(msg)
docv = np.vstack([g[k]["V"][:] for k in corpus_keys])
return {
"docv" : docv,
"_refs": _refs
}
def __init__(self, *args, **kwargs):
'''
Computes various measures of central tendency of a document.
For Z_X scores, the raw word tokens are summed over the partition
function. For I_X scores, the same statistics are computed over
the similarity of all word pairs for words with top 10% Z values.
This will precompute the partition function if it doesn't exist.
'''
cfg_embed = simple_config.load()["embedding"]
cfg_score = simple_config.load()["score"]
f_w2v = os.path.join(
cfg_embed["output_data_directory"],
cfg_embed["w2v_embedding"]["f_db"],
)
f_partition_function = os.path.join(
cfg_embed["output_data_directory"],
cfg_score["document_log_probability"]["f_partition_function"],
)
if not os.path.exists(f_partition_function):
self.create_partition_function(f_w2v, f_partition_function)
self.Z = self.load_partition_function(f_partition_function)
self.scores = []
val = cfg_score["document_log_probability"]["intra_document_cutoff"]
self.intra_document_cutoff = float(val)
self.model = load_w2vec()
def __init__(self, *args, **kwargs):
super(generic_document_score, self).__init__(*args, **kwargs)
# Load the model from disk
self.M = load_w2vec()
self.shape = self.M.wv.syn0.shape
# Build the dictionary
vocab_n = self.shape[0]
self.word2index = dict(zip(self.M.wv.index2word, range(vocab_n)))
# Set parallel option (currently does nothing)
# self._PARALLEL = kwargs["_PARALLEL"]
if "negative_weights" in kwargs:
NV = []
for word, weight in kwargs["negative_weights"].items():
if not self.check_word_vector(word):
msg = "Negative weight word '{}' not found in dictionary"
print(msg.format(word))
continue
vec = self.get_word_vector(word)
scale = np.exp(-float(weight) * self.M.wv.syn0.dot(vec))
# Don't oversample, max out weights to unity
scale[scale > 1] = 1.0
NV.append(scale)
self.negative_weights = np.array(NV).T.sum(axis=1)
else:
self.negative_weights = np.ones(vocab_n, dtype=float)
# Save the target column to compute
self.target_column = simple_config.load()["target_column"]
# Make sure nothing has been set yet
self.V = self._ref = None
# Set the variables for reduced representation
config_score = simple_config.load()["score"]
self.compute_reduced = config_score["compute_reduced_representation"]
if self.compute_reduced:
sec = config_score['reduced_representation']
self.reduced_n_components = sec['n_components']
self.h5py_args = {"compression": "gzip"}
def load_ORG_data(extra_columns=None):
print("Loading import data")
cols = [
"_ref",
]
if extra_columns is not None:
cols += extra_columns
config_import = simple_config.load()["import_data"]
# Load the input columns
F_CSV = grab_files("*.csv", config_import["output_data_directory"])
ITR = (pd.read_csv(f, usecols=cols) for f in F_CSV)
df = pd.concat(list(ITR))
# Require the _refs to be in order as a sanity check
if not (np.sort(df._ref) == df._ref).all():
msg = "WARNING, data out of sort order from _refs"
raise ValueError(msg)
df = df.set_index('_ref')
df['_ref'] = df.index
return df
def load_document_vectors(score_method, use_reduced=False):
config_score = simple_config.load()["score"]
f_h5 = os.path.join(
config_score["output_data_directory"],
config_score['document_scores']["f_db"],
)
with h5py.File(f_h5, 'r') as h5:
assert (score_method in h5)
g = h5[score_method]
_refs = np.hstack([g[k]["_ref"][:] for k in g.keys()])
vector_key = "VX" if use_reduced else "V"
X = np.vstack([g[k][vector_key][:] for k in g.keys()])
assert (X.shape[0] == _refs.size)
# Sort to the proper order
sort_idx = np.argsort(_refs)
_refs = _refs[sort_idx]
X = np.vstack(X)[sort_idx]
return {"docv": X, "_refs": _refs}
def load_ORG_data(extra_columns=None):
print("Loading import data")
cols = [
"_ref",
]
if extra_columns is not None:
cols += extra_columns
config = simple_config.load()
config_import = config["import_data"]
CORES = -1 if config["_PARALLEL"] else 1
# Load the input columns
F_CSV = grab_files("*.csv", config_import["output_data_directory"])
with joblib.Parallel(CORES) as MP:
func = joblib.delayed(simple_CSV_read)
data = MP(func(x, cols) for x in F_CSV)
# Require the _refs to be in order
df = pd.concat(data).sort_values('_ref').set_index('_ref')
# Use _ref as an index, but keep it as a row
df['_ref'] = df.index
return df
def main():
args = docopt(__doc__)
config = simple_config.load()
if args["import_data"]:
import_data_from_config(config)
phrases_from_config(config)
if args["parse"]:
parse_from_config(config)
if args["embed"]:
embed_from_config(config)
if args["score"]:
score_from_config(config)
if args["predict"]:
predict_from_config(config)
if args["metacluster"]:
metacluster_from_config(config)
if args["analyze"]:
func = args["<target_function>"]
if func == 'metacluster':
analyze_metacluster_from_config(config)
else:
raise KeyError("Analyze Function {} not known".format(func))
def load_ORG_data(extra_columns=None):
"""
DOCUMENTATION_UNKNOWN
"""
logger.info("Loading original data")
cols = []
if extra_columns is not None:
cols += extra_columns
config = simple_config.load()
config_import = config["import_data"]
CORES = -1 if config["_PARALLEL"] else 1
# Load the input columns
F_CSV_REF = grab_files("*.csv", config_import["output_data_directory"])
F_CSV = grab_files("*.csv", config_import["input_data_directories"][0])
with joblib.Parallel(CORES) as MP:
func = joblib.delayed(simple_CSV_read)
data = MP(func(x, cols) for x in F_CSV)
_refs = MP(func(x, ["_ref"]) for x in F_CSV_REF)
for df, df_refs in zip(data, _refs):
df["_ref"] = df_refs["_ref"].values
# Require the _refs to be in order
df = pd.concat(data).sort_values("_ref").set_index("_ref")
# Use _ref as an index, but keep it as a row
df["_ref"] = df.index
return df
def save_single(self):
assert (self.V is not None)
assert (self._ref is not None)
# Set the size explictly as a sanity check
size_n, dim_V = self.V.shape
config_score = simple_config.load()["score"]
f_db = os.path.join(config_score["output_data_directory"],
config_score["document_scores"]["f_db"])
h5 = touch_h5(f_db)
g = h5.require_group(self.method)
gx = g.require_group(self.current_filename)
# Save the data array
msg = "Saving {} {} ({})"
print(msg.format(self.method, self.current_filename, size_n))
for col in [
"V", "_ref", "VX", "VX_explained_variance_ratio_",
"VX_components_"
]:
if col in gx:
#print " Clearing", self.method, self.current_filename, col
del gx[col]
gx.create_dataset("V", data=self.V, **self.h5py_args)
gx.create_dataset("_ref", data=self._ref, **self.h5py_args)
def load_metacluster_data(*args):
config_metacluster = simple_config.load()["metacluster"]
f_h5 = os.path.join(config_metacluster["output_data_directory"],
config_metacluster["f_centroids"])
return load_h5_file(f_h5, *args)
def item_iterator(
config=None,
randomize_file_order=False,
whitelist=[],
section='parse',
progress_bar=False,
text_column=None,
include_filename=False,
):
'''
Iterates over the parsed corpus items and respects a given whitelist.
'''
if config is None:
config = simple_config.load()
config = simple_config.load()
input_data_dir = config['parse']["output_data_directory"]
F_CSV = grab_files("*.csv", input_data_dir, verbose=False)
if whitelist:
assert(isinstance(whitelist, list))
F_CSV2 = set()
for f_csv in F_CSV:
for token in whitelist:
if token in f_csv:
F_CSV2.add(f_csv)
F_CSV = F_CSV2
# Randomize the order of the input files each time we get here
if randomize_file_order:
F_CSV = random.sample(sorted(F_CSV), len(F_CSV))
INPUT_ITR = CSV_database_iterator(
F_CSV,
config["target_column"],
progress_bar=progress_bar,
include_filename=include_filename,
)
for row in INPUT_ITR:
if text_column is not None:
row['text'] = row[text_column]
yield row
def load_metacluster_data(*args):
config_metacluster = simple_config.load("metacluster")
f_h5 = os.path.join(
config_metacluster["output_data_directory"],
config_metacluster["f_centroids"])
return load_h5_file(f_h5, *args)
def __init__(self):
config = simple_config.load("metacluster")
self.subcluster_m = int(config["subcluster_m"])
self.subcluster_pcut = float(config["subcluster_pcut"])
self.subcluster_repeats = int(config["subcluster_repeats"])
self.subcluster_kn = int(config["subcluster_kn"])
config_score = simple_config.load("score")
self.f_h5_docvecs = os.path.join(config_score["output_data_directory"], config_score["document_scores"]["f_db"])
self.f_h5_centroids = os.path.join(config["output_data_directory"], config["f_centroids"])
score_method = config["score_method"]
text_column = config["score_column"]
self._load_data(self.f_h5_docvecs, score_method, text_column)
def load_dispersion_data():
print "Loading dispersion data"
config_post = simple_config.load("postprocessing")
f_h5 = os.path.join(
config_post["output_data_directory"],
"cluster_dispersion.h5")
return load_h5_file(f_h5)
def get_score_methods():
config_score = simple_config.load()["score"]
f_h5 = os.path.join(
config_score["output_data_directory"],
config_score['document_scores']["f_db"],
)
with h5py.File(f_h5, 'r') as h5:
return h5.keys()
def load_w2vec(config=None):
if config is None:
config = simple_config.load()
config_embed = config["embedding"]
f_w2v = os.path.join(
config_embed["output_data_directory"],
config_embed["w2v_embedding"]["f_db"],
)
return W2V.Word2Vec.load(f_w2v)
def get_section_filenames(section='parse'):
'''
Grab filenames in given section of pipeline.
Args:
section (str): The section to grab the filenames (default: parse)
Returns:
list: files found in directory specified in config
'''
config = simple_config.load()
input_data_dir = config[section]["output_data_directory"]
return grab_files("*.csv", input_data_dir)
def load_embeddings():
'''
Loads the gensim word embedding model.
'''
config = simple_config.load("embedding")
from gensim.models.word2vec import Word2Vec
f_w2v = os.path.join(
config["output_data_directory"],
config["w2v_embedding"]["f_db"],
)
return Word2Vec.load(f_w2v)
def __init__(self, *args, **kwargs):
super(generic_document_score, self).__init__(*args, **kwargs)
# Load the model from disk
self.M = load_w2vec()
self.shape = self.M.syn0.shape
# Build the dictionary
vocab_n = self.shape[0]
self.word2index = dict(zip(self.M.index2word, range(vocab_n)))
# Set parallel option (currently does nothing)
# self._PARALLEL = kwargs["_PARALLEL"]
# Load the negative weights
if "negative_weights" in kwargs:
neg_W = kwargs["negative_weights"]
self.neg_W = dict((k, float(v)) for k, v in neg_W.items())
self.neg_vec = dict((k, self.get_word_vector(k))
for k, v in neg_W.items())
else:
self.neg_W = {}
self.neg_vec = {}
# Save the target column to compute
self.target_column = simple_config.load()["target_column"]
# Make sure nothing has been set yet
self.V = self._ref = None
# Set the variables for reduced representation
config_score = simple_config.load()["score"]
self.compute_reduced = config_score["compute_reduced_representation"]
if self.compute_reduced:
sec = config_score['reduced_representation']
self.reduced_n_components = sec['n_components']
def __init__(self):
config = simple_config.load()["metacluster"]
self.subcluster_m = int(config["subcluster_m"])
self.subcluster_pcut = float(config["subcluster_pcut"])
self.subcluster_repeats = int(config["subcluster_repeats"])
self.subcluster_kn = int(config["subcluster_kn"])
config_score = simple_config.load()["score"]
self.f_h5_docvecs = os.path.join(
config_score["output_data_directory"],
config_score['document_scores']["f_db"],
)
self.f_h5_centroids = os.path.join(
config["output_data_directory"],
config["f_centroids"],
)
score_method = config['score_method']
self._load_data(self.f_h5_docvecs, score_method)
def get_score_methods():
'''
Determines which scoring methods to return for each document,
based on what's set in config file
Returns:
h5.keys(): DOCUMENTATION_UNKNOWN
'''
config_score = simple_config.load()["score"]
f_h5 = os.path.join(
config_score["output_data_directory"],
config_score["f_db"],
)
with h5py.File(f_h5, 'r') as h5:
return h5.keys()
def item_iterator(name,cmd_config=None):
score_config = simple_config.load("parse")
input_data_dir = score_config["output_data_directory"]
F_SQL = glob.glob(os.path.join(input_data_dir,'*'))
# If there is a whitelist only keep the matching filename
try:
whitelist = cmd_config["command_whitelist"].strip()
except:
whitelist = None
if whitelist:
assert(type(whitelist)==list)
F_SQL2 = set()
for f_sql in F_SQL:
for token in whitelist:
if token in f_sql:
F_SQL2.add(f_sql)
F_SQL = F_SQL2
# Randomize the order of the input files
F_SQL = random.sample(sorted(F_SQL), len(F_SQL))
DB_ITR = itertools.product(F_SQL, config["target_columns"])
for f_sql, target_col in DB_ITR:
#print ("Computing {}:{}".format(f_sql, target_col))
conn = sqlite3.connect(f_sql, check_same_thread=False)
args = {
"column_name":"text",
"table_name" :target_col,
"conn":conn,
"limit":_global_limit,
"shuffle":False,
"include_table_name":True,
}
INPUT_ITR = database_iterator(**args)
for item in INPUT_ITR:
yield list(item) + [f_sql,]
def save(self):
assert(self.V is not None)
assert(self._ref is not None)
# Set the size explictly as a sanity check
size_n, dim_V = self.V.shape
# print "Saving the scored documents"
config_score = simple_config.load()["score"]
f_db = os.path.join(
config_score["output_data_directory"],
config_score["document_scores"]["f_db"]
)
h5 = touch_h5(f_db)
# Clear the dataset if it already exists
if self.method in h5:
del h5[self.method]
g = h5.require_group(self.method)
# Save the data array
print("Saving {} ({})".format(self.method, size_n))
g.create_dataset("V", data=self.V, compression='gzip')
g.create_dataset("_ref", data=self._ref)
# Compute the reduced representation if required
if self.compute_reduced:
nc = self.reduced_n_components
clf = IncrementalPCA(n_components=nc)
msg = "Performing PCA on {}, ({})->({})"
print(msg.format(self.method, self.V.shape[1], nc))
VX = clf.fit_transform(self.V)
g.create_dataset("VX", data=VX, compression='gzip')
g.create_dataset("VX_explained_variance_ratio_",
data=clf.explained_variance_ratio_)
g.create_dataset("VX_components_",
data=clf.components_)
h5.close()
def __init__(self):
config = simple_config.load()["metacluster"]
self.subcluster_m = int(config["subcluster_m"])
self.subcluster_pcut = float(config["subcluster_pcut"])
self.subcluster_repeats = int(config["subcluster_repeats"])
self.subcluster_kn = int(config["subcluster_kn"])
self.f_h5_centroids = os.path.join(config["output_data_directory"],
config["f_centroids"])
score_method = config["score_method"]
DV = uds.load_document_vectors(score_method)
self._ref = DV["_refs"]
self.docv = DV["docv"]
self.N, self.dim = self.docv.shape
def main():
args = docopt(__doc__)
config = simple_config.load()
if args["import_data"]:
from import_data import import_data_from_config
import_data_from_config(config)
elif args["phrase"]:
from phrase import phrases_from_config
phrases_from_config(config)
if args["parse"]:
from parse import parse_from_config
parse_from_config(config)
if args["embed"]:
from embed import embed_from_config
embed_from_config(config)
if args["score"]:
from score import score_from_config
score_from_config(config)
if args["predict"]:
from predict import predict_from_config
predict_from_config(config)
if args["metacluster"]:
from metacluster import metacluster_from_config
metacluster_from_config(config)
if args["analyze"]:
import postprocessing.analyze_metaclusters as pam
pam.analyze_metacluster_from_config(config)
def load_document_vectors(score_method, use_reduced=False):
'''
Load the word2vec document vectors for each document from the h5 file
saved in pipeline
Args:
score_method: string, score method to load
use_reduced: boolean, flag to determine whether to use reduced
dimension vectors, or the orgiginal vectors
Return:
{"docv": X, "_refs": _refs}: dictionary, contains a list of document
vectors and corresponding references
'''
config_score = simple_config.load()["score"]
f_h5 = os.path.join(
config_score["output_data_directory"],
config_score["f_db"],
)
with h5py.File(f_h5, 'r') as h5:
assert(score_method in h5)
g = h5[score_method]
_refs = np.hstack([g[k]["_ref"][:] for k in g.keys()])
vector_key = "VX" if use_reduced else "V"
X = np.vstack([g[k][vector_key][:] for k in g.keys()])
assert(X.shape[0] == _refs.size)
# Sort to the proper order
sort_idx = np.argsort(_refs)
_refs = _refs[sort_idx]
X = np.vstack(X)[sort_idx]
return {
"docv": X,
"_refs": _refs
}
def load_metacluster_data(*args):
'''
Load information on metaclusters from where they're saved in the pipeline
Args:
*args: DOCUMENTATION_UNKNOWN
Returns:
load_h5_file(f_h5, *args): the data on each cluster found in the
h5 file
'''
config_metacluster = simple_config.load()["metacluster"]
f_h5 = os.path.join(
config_metacluster["output_data_directory"],
config_metacluster["f_centroids"])
return load_h5_file(f_h5, *args)
def main():
args = docopt(__doc__)
config = simple_config.load()
if args["import_data"]:
from import_data import import_data_from_config
import_data_from_config(config)
elif args["phrase"]:
from phrase import phrases_from_config
phrases_from_config(config)
if args["parse"]:
from parse import parse_from_config
parse_from_config(config)
if args["embed"]:
from embed import embed_from_config
embed_from_config(config)
if args["score"]:
from score import score_from_config
score_from_config(config)
if args["predict"]:
from predict import predict_from_config
predict_from_config(config)
if args["metacluster"]:
from metacluster import metacluster_from_config
metacluster_from_config(config)
if args["analyze"]:
func = args["<target_function>"]
if func == 'metacluster':
import postprocessing.analyze_metaclusters as pam
pam.analyze_metacluster_from_config(config)
elif func == 'LIME':
import postprocessing.lime_explainer as le
le.explain_metaclusters(config)
else:
raise KeyError("Analyze Function {} not known".format(func))
def get_score_methods():
"""
Determines which scoring methods to return for each document,
based on what's set in config file.
Returns:
h5.keys(): DOCUMENTATION_UNKNOWN
"""
config_score = simple_config.load()["score"]
f_h5 = os.path.join(config_score["output_data_directory"],
config_score["f_db"])
if not os.path.exists(f_h5):
raise FileNotFoundError(f_h5)
with h5py.File(f_h5, "r") as h5:
keys = list(h5.keys())
return keys
def __init__(self, name, cmd_config=None, yield_single=False):
# yield_single returns one item at a time,
# not in chunks like (table_name, f_sql)
self.yield_single = yield_single
score_config = simple_config.load("parse")
input_data_dir = score_config["output_data_directory"]
F_SQL = sorted(glob.glob(os.path.join(input_data_dir,'*')))
# If there is a whitelist only keep the matching filename
try:
whitelist = cmd_config["command_whitelist"].strip()
except:
whitelist = None
if whitelist:
assert(type(whitelist)==list)
F_SQL2 = set()
for f_sql in F_SQL:
for token in whitelist:
if token in f_sql:
F_SQL2.add(f_sql)
F_SQL = F_SQL2
# Randomize the order of the input files (why? not needed for scoring)
# F_SQL = random.sample(sorted(F_SQL), len(F_SQL))
DB_ITR = itertools.product(F_SQL, config["target_columns"])
# Get database sizes for progress bar
self.total_items = 0
for f_sql, target_col in DB_ITR:
conn = sqlite3.connect(f_sql, check_same_thread=False)
self.total_items += count_rows(conn, target_col)
conn.close()
self.F_SQL = F_SQL
self.config = config
def __init__(self, *args, **kwargs):
super(score_simple, self).__init__(*args, **kwargs)
f_db = os.path.join(kwargs['output_data_directory'],
kwargs['term_frequency']['f_db'])
if not os.path.exists(f_db):
msg = "{} not computed yet, needed for TF methods!"
raise ValueError(msg.format(f_db))
score_config = simple_config.load()["score"]
f_csv = os.path.join(
score_config["output_data_directory"],
score_config["term_document_frequency"]["f_db"],
)
IDF = pd.read_csv(f_csv)
IDF = dict(zip(IDF["word"].values, IDF["count"].values))
self.corpus_N = IDF.pop("__pipeline_document_counter")
# Compute the IDF
for key in IDF:
IDF[key] = np.log(float(self.corpus_N) / (IDF[key] + 1))
self.IDF = IDF
def __init__(self, *args, **kwargs):
'''
The reduced representation takes an incremental PCA decomposition
and adds new negative weights based off the previous components
of PCA.
'''
# Remove the bais to negative_weights
kwargs["negative_weights"] = {}
super(reduced_representation, self).__init__(*args, **kwargs)
config = simple_config.load()['score']
f_db = os.path.join(
config["output_data_directory"],
config["document_scores"]["f_db"]
)
with h5py.File(f_db, 'r') as h5:
# Make sure the the column has a value
col = config['reduced_representation']['rescored_command']
assert(col in h5)
# Make sure the VX has been computed
assert("VX" in h5[col])
c = h5[col]['VX_components_'][:]
ex_var = h5[col]['VX_explained_variance_ratio_'][:]
bais = config['reduced_representation']['bais_strength']
self.word_vecs = {}
for w in self.M.wv.index2word:
weight = c.dot(self.M[w])
weight *= bais
weight *= ex_var
adjust_v = (weight.reshape(-1, 1) * c).sum(axis=0)
self.word_vecs[w] = self.M[w] - adjust_v
def compute_reduced_representation(self):
if not self.compute_reduced:
return None
config_score = simple_config.load()["score"]
f_db = os.path.join(config_score["output_data_directory"],
config_score["document_scores"]["f_db"])
h5 = touch_h5(f_db)
g = h5[self.method]
keys = g.keys()
V = np.vstack([g[x]["V"][:] for x in keys])
sizes = [g[x]["_ref"].shape[0] for x in keys]
nc = self.reduced_n_components
clf = IncrementalPCA(n_components=nc)
msg = "Performing PCA on {}, ({})->({})"
print(msg.format(self.method, V.shape[1], nc))
VX = clf.fit_transform(V)
EVR = clf.explained_variance_ratio_
COMPONENTS = clf.components_
for key, size in zip(keys, sizes):
# Take slices equal to the size
vx, VX = VX[:size, :], VX[size:, :]
evr, EVR = EVR[:size], EVR[size:]
com, COMPONENTS = COMPONENTS[:size, :], COMPONENTS[size:, :]
g[key].create_dataset("VX", data=vx, **self.h5py_args)
g[key].create_dataset("VX_explained_variance_ratio_", data=evr)
g[key].create_dataset("VX_components_", data=com)
h5.close()
def load_w2vec(config=None):
"""
Loads gensim word2vec model saved in pipeline.
Args:
config: config file to get parameters from
Returns:
W2V.Word2Vec.load(f_w2v): gensim word2vec model
"""
import gensim.models.word2vec as W2V
if config is None:
config = simple_config.load()
config_embed = config["embed"]
f_w2v = os.path.join(
config_embed["output_data_directory"],
config_embed["w2v_embedding"]["f_db"],
)
return W2V.Word2Vec.load(f_w2v)
"""
merge_columns = config["import_data"]["merge_columns"]
if not isinstance(merge_columns, list):
msg = "merge_columns (if used) must be a list"
raise ValueError(msg)
data_out = config["import_data"]["output_data_directory"]
mkdir(data_out)
# Require 'input_data_directories' to be a list
data_in_list = config["import_data"]["input_data_directories"]
if not isinstance(data_in_list, list):
msg = "input_data_directories must be a list"
raise ValueError(msg)
target_column = config["target_column"]
for d_in in data_in_list:
import_directory_csv(d_in, data_out, target_column, merge_columns)
if __name__ == "__main__":
import simple_config
config = simple_config.load()
import_data_from_config(config)
"column_name":"text",
"table_name" :target_col,
"conn":conn,
"limit":_global_limit,
"shuffle":False,
"include_table_name":True,
}
INPUT_ITR = database_iterator(**args)
for item in INPUT_ITR:
yield list(item) + [f_sql,]
if __name__ == "__main__":
import simple_config
config = simple_config.load("embedding")
_FORCE = config.as_bool("_FORCE")
mkdir(config["output_data_directory"])
###########################################################
# Run the functions that act globally on the data
for name in config["embedding_commands"]:
obj = getattr(mb,name)
# Load any kwargs in the config file
kwargs = config
if name in config:
kwargs.update(config[name])
for f in parser_functions:
result = f(text)
text = unicode(result)
if hasattr(result,"meta"):
meta.update(result.meta)
# Convert the meta information into a unicode string for serialization
meta = unicode(meta)
return idx, text, meta
if __name__ == "__main__":
import simple_config
config = simple_config.load("parse")
_PARALLEL = config.as_bool("_PARALLEL")
_FORCE = config.as_bool("_FORCE")
import_config = simple_config.load("import_data")
input_data_dir = import_config["output_data_directory"]
output_dir = config["output_data_directory"]
import_column = import_config["output_table"]
mkdir(output_dir)
# Fill the pipeline with function objects
parser_functions = []
for name in config["pipeline"]:
obj = getattr(pre,name)
for i in range(n_clusters):
v = meta_clusters[i]
dist = W.syn0.dot(v)
idx = np.argsort(dist)[::-1][:10]
words = [W.index2word[i].replace("PHRASE_", "") for i in idx]
all_words.append(u" ".join(words))
return np.array(all_words)
if __name__ == "__main__":
config = simple_config.load("metacluster")
os.system("mkdir -p {}".format(config["output_data_directory"]))
CO = cluster_object()
f_h5 = CO.f_h5_centroids
if not os.path.exists(f_h5):
h5 = h5py.File(f_h5, "w")
h5.close()
h5 = h5py.File(f_h5, "r+")
keys = ["subcluster_kn", "subcluster_pcut", "subcluster_m", "subcluster_repeats"]
args = dict([(k, config[k]) for k in keys])
val = list(item) + [f_sql,]
data.append(val)
if self.yield_single:
for item in INPUT_ITR:
val = list(item) + [f_sql,]
yield val
progress_bar.update()
if not self.yield_single:
yield data
if __name__ == "__main__":
import simple_config
config = simple_config.load("score")
_PARALLEL = config.as_bool("_PARALLEL")
_FORCE = config.as_bool("_FORCE")
n_jobs = -1 if _PARALLEL else 1
mkdir(config["output_data_directory"])
###########################################################
# Fill the pipeline with function objects
mapreduce_functions = []
for name in config["mapreduce_commands"]:
obj = getattr(ds,name)
n_data_items = len(df)
df["_ref"] = [_ref_counter.next()
for _ in range(n_data_items)]
df.set_index("_ref",inplace=True)
df.to_sql(output_table,
engine,
if_exists='replace')
print "Finished {}, {}, {}".format(f_csv, len(df), list(df.columns))
if __name__ == "__main__":
import simple_config
config = simple_config.load("import_data")
_PARALLEL = config.as_bool("_PARALLEL")
_FORCE = config.as_bool("_FORCE")
data_out = config["output_data_directory"]
output_table = config["output_table"]
# Require `input_data_directories` to be a list
data_in_list = config["input_data_directories"]
assert(type(data_in_list) == list)
for d_in in data_in_list:
import_directory_csv(d_in, data_out, output_table)
if config["command_whitelist"]:
keys = [k for k in keys if k in config["command_whitelist"]]
print "Only computing over", keys
X = np.vstack(g[key]["V"] for key in keys)
h5_score.close()
return X
if __name__ == "__main__":
import simple_config
config = simple_config.load("cluster")
output_dir = config["output_data_directory"]
mkdir(output_dir)
method = config['score_method']
target_column = config['score_column']
f_sim = os.path.join(output_dir, config["f_cluster"])
if config.as_bool("_FORCE"):
try:
os.remove(f_sim)
except:
pass
if not os.path.exists(f_sim):
total_counts += current_val
if current_val > max_val:
max_val = current_val
max_item = item
data[(' '.join(max_item[0]), max_item[1])] = total_counts
ABR = collections.Counter(data)
return ABR
if __name__ == "__main__":
import simple_config
config = simple_config.load("phrase_identification")
_PARALLEL = config.as_bool("_PARALLEL")
_FORCE = config.as_bool("_FORCE")
output_dir = config["output_data_directory"]
target_columns = config["target_columns"]
import_config = simple_config.load("import_data")
input_data_dir = import_config["output_data_directory"]
input_table = import_config["output_table"]
F_SQL = grab_files("*.sqlite", input_data_dir)
ABR = collections.Counter()
P = parenthesis_nester()
import numpy as np
import pandas as pd
import h5py
import os, glob, itertools, collections
from sqlalchemy import create_engine
from predictions import categorical_predict
ERROR_MATRIX = {}
PREDICTIONS = {}
if __name__ == "__main__":
import simple_config
config = simple_config.load("predict")
score_config = simple_config.load("score")
import_config = simple_config.load("import_data")
# For now, we can only deal with one column using meta!
assert len(config["categorical_columns"]) == 1
f_h5 = os.path.join(score_config["output_data_directory"], score_config["document_scores"]["f_db"])
h5 = h5py.File(f_h5, "r")
methods = h5.keys()
pred_dir = import_config["output_data_directory"]
input_glob = os.path.join(pred_dir, "*")
input_files = glob.glob(input_glob)
if i==j:
d = pdist(X[labels==i],metric='cosine')
else:
d = cdist(X[labels==i],X[labels==j],metric='cosine')
# Only take upper diagonal (+diagonal elements)
d = d[np.triu_indices(n=d.shape[0],m=d.shape[1],k=0)]
dist[i,j] = dist[j,i] = d.mean()
return dist
if __name__ == "__main__" and __package__ is None:
import simple_config
config = simple_config.load("postprocessing")
save_dest = config['output_data_directory']
os.system('mkdir -p {}'.format(save_dest))
SQL = load_SQL_data(config["master_columns"])
MC = load_metacluster_data()
C = MC["meta_centroids"]
counts = collections.Counter(MC["meta_labels"])
DV = load_document_vectors()
# Build the results for the metaclusters
labels = np.unique(MC["meta_labels"])