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How to use section_logger method in molecule

Best Python code snippet using molecule_python

visualgenome.py

Source:visualgenome.py

...51            "|".join(r['synsets'])52        ]53    return extractor54def extract_relationship_dataframe(vg, limit=10, report=2e5):55    section = section_logger(1)56    data = []57    counter = 058    for img in vg['relationships']:59        if counter > limit:60            break61        else:62            counter += 163        if counter % report == 0:64            section("Loaded relationships in {} images".format(counter))65        rows = map(extract_relationship_data(img['image_id']), img['relationships'])66        data.extend(list(rows))67    rdf = pd.DataFrame(data, columns=['img', 'object', 'subject', 'predicate', 'synsets'])68    return rdf69def extract_object_data(img_id, img_w, img_h):70    def extractor(obj):71        return [72            obj['object_id'],73            "|".join(obj['synsets']),74            "|".join(obj['names']),75            img_id,76            obj['x']/img_w,77            obj['y']/img_h,78            obj['h']/img_h,79            obj['w']/img_w80        ]81    return extractor82def extract_object_dataframe(vg, limit=10, report=2e5):83    section = section_logger(1)84    data = []85    counter = 086    for img in vg['objects']:87        if counter > limit:88            break89        else:90            counter += 191        if counter % report == 0:92            section("Loaded objects in {} images".format(counter))93        current_image = vg['imageIdMap'][img['image_id']]94        assert current_image['image_id'] == img['image_id'], 'Position in the list {} does not correspond to ID {}'.format(img['image_id'], current_image['image_id'])95        rows = map(extract_object_data(img['image_id'], current_image['width'], current_image['height']), img['objects'])96        data.extend(rows)97    odf = pd.DataFrame(data, columns=['object_id', 'synsets', 'names', 'img', 'x', 'y', 'h', 'w'])98    return odf99def add_key_to_dict(id, collection):100    if id in collection:101        id_obj = collection[id]102    else:103        id_obj = len(collection)104        collection[id] = id_obj105    return id_obj106def extract_knowledge_graph(vg, limit=10, report=2e5):107    section = section_logger(1)108    counter = 0109    synset_ids = {}110    knowledge_graph = nx.DiGraph()111    for img in vg['relationships']:112        if counter > limit:113            break114        else:115            counter += 1116        if counter % report == 0:117            section("Loaded relationships in {} images".format(counter))118        for r in img['relationships']:119            object = r['object']['synsets']120            subject = r['subject']['synsets']121            predicate = r['synsets']122            for syn_obj in object:123                for syn_sub in subject:124                    id_obj = add_key_to_dict(syn_obj, synset_ids)125                    id_sub = add_key_to_dict(syn_sub, synset_ids)126                    if len(predicate) == 1:127                        predicate_str = predicate[0]128                    else:129                        predicate_str = 'relation.n.01'130                    knowledge_graph.add_edge(id_obj, id_sub, predicate=predicate_str)131    return knowledge_graph, synset_ids132def extract_data_analytics():133    section = section_logger()134    section('Extracting Visual Genome')135    vg = load_visual_genome()136    section('Generating DataFrames from the object files')137    odf = extract_object_dataframe(vg, int(1e6))138    section('Generating DataFrames from the relationship files')139    rdf = extract_relationship_dataframe(vg, int(1e6))140    section('Saving CSVs')141    odf.to_csv(os.path.join(cf.VG_ANALYTICS, 'vg_objects.csv'))142    rdf.to_csv(os.path.join(cf.VG_ANALYTICS, 'vg_relationships.csv'))143def extract_relations_wordnet(graph, syn_id, synset_ids, wordnet_syn, relation, predicate):144    hypernyms = wordnet_syn.__getattribute__(relation)()145    for hyp in hypernyms:146        hyp_name = hyp.name()147        if hyp_name in synset_ids:148            hyp_id = synset_ids[hyp_name]149        else:150            hyp_id = add_key_to_dict(hyp_name, synset_ids)151        graph.add_edge(syn_id, hyp_id, predicate=predicate)152    return graph, synset_ids153def add_wordnet_synsets(graph, synset_ids, report=2e5):154    old_synset_ids = dict(synset_ids)155    section = section_logger(1)156    counter = 0157    for syn_name, syn_id in old_synset_ids.items():158        counter += 1159        if counter % report == 0:160            section("Loaded relationships in {} images".format(counter))161        wordnet_syn = wordnet.synset(syn_name)162        extract_relations_wordnet(graph, syn_id, synset_ids, wordnet_syn, 'hypernyms', 'generalize.v.01')163        extract_relations_wordnet(graph, syn_id, synset_ids, wordnet_syn, 'hyponyms', 'specialize.v.01')164    return graph, synset_ids165def save_graph_info(graph, ids):166    nx.write_gml(graph, os.path.join(cf.VG_ANALYTICS, 'knowledge_graph.gml'))167    with open(os.path.join(cf.VG_ANALYTICS, 'synset_ids.json'), 'w') as outfile:168        json.dump(ids, outfile)169def compute_knowledge_graph():170    section = section_logger()171    section('Loading JSON files from dataset')172    vg = load_visual_genome()173    section('Generating Knowledge Graph')174    vi_graph, synset_ids = extract_knowledge_graph(vg, limit=1e10)175    section('Annotating with Wordnet synsets')176    wn_graph, synset_ids = add_wordnet_synsets(vi_graph, synset_ids)177    section('Saving graph')178    save_graph_info(wn_graph, synset_ids)179    return wn_graph180def load_graph_info():181    wn_graph = nx.read_gml(os.path.join(cf.VG_ANALYTICS, 'knowledge_graph.gml'))182    with open(os.path.join(cf.VG_ANALYTICS, 'synset_ids.json'), 'r') as infile:183        ids = json.load(infile)184    return wn_graph, ids...

settings.py

Source:settings.py

1"""2Django settings for redbutterfly project.3Generated by 'django-admin startproject' using Django 1.10.4For more information on this file, see5https://docs.djangoproject.com/en/1.10/topics/settings/6For the full list of settings and their values, see7https://docs.djangoproject.com/en/1.10/ref/settings/8"""9import os10import logging11from util.log_util import *12# Build paths inside the project like this: os.path.join(BASE_DIR, ...)13BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))14SECRET_KEY = 'mpjq@%1+hv@j90oxs0spt&9#4xeg0#g_n&9nnb)v_$-oz4!39$'15DEBUG = True16ALLOWED_HOSTS = ['*']17#default ini18DEFAULT_CONFIG_FILE = os.path.join(BASE_DIR, "conf/server.ini")19SECTION_REDIS = 'redis_server'20SECTION_LOGGER = 'server_log'21#logger info define22SERVICE_LOGGERFILE = os.path.join(BASE_DIR, "log/project_log/service.log")23CreatLogger('server', SERVICE_LOGGERFILE, SECTION_LOGGER)24server_logger = logging.getLogger('server')25# Application definition26INSTALLED_APPS = [27    'django.contrib.admin',28    'django.contrib.auth',29    'django.contrib.contenttypes',30    'django.contrib.sessions',31    'django.contrib.messages',32    'django.contrib.staticfiles',33    'rest_framework',34    'red',35]36MIDDLEWARE_CLASSES = [37    'django.middleware.security.SecurityMiddleware',38    'django.contrib.sessions.middleware.SessionMiddleware',39    'django.middleware.locale.LocaleMiddleware',40    'django.middleware.common.CommonMiddleware',41    'django.middleware.csrf.CsrfViewMiddleware',42    'django.contrib.auth.middleware.AuthenticationMiddleware',43    'django.contrib.auth.middleware.SessionAuthenticationMiddleware',44    'django.contrib.messages.middleware.MessageMiddleware',45    'django.middleware.clickjacking.XFrameOptionsMiddleware',46]47ROOT_URLCONF = 'conf.urls'48TEMPLATES = [49    {50        'BACKEND': 'django.template.backends.django.DjangoTemplates',51        'DIRS': [os.path.join(BASE_DIR,'templates')],52        'APP_DIRS': True,53        'OPTIONS': {54            'context_processors': [55                'django.template.context_processors.debug',56                'django.template.context_processors.request',57                'django.contrib.auth.context_processors.auth',58                'django.contrib.messages.context_processors.messages',59            ],60        },61    },62]63TEMPLATE_CONTEXT_PROCESSORS = (64        "django.template.context_processors.request",65	"django.contrib.auth.context_processors.auth",66	"django.template.context_processors.debug",67	"django.template.context_processors.i18n",68	"django.template.context_processors.media",69	"django.template.context_processors.static",70	"django.template.context_processors.tz",71	"django.contrib.messages.context_processors.messages"72)73WSGI_APPLICATION = 'conf.wsgi.application'74DATABASES = {75    'default': {76        'ENGINE': 'django.db.backends.mysql',77        'NAME': 'redbutterfly',78	'USER':	'root',79	'PASSWORD': '426334',80	'HOST': '',81	'PORT': '',82    }83}84CACHES = {85    'default': {86        'BACKEND': 'django_redis.cache.RedisCache',87        'LOCATION': 'redis://127.0.0.1:6379/2',88	'OPTIONS': {89	    'CLIENT_CLASS': 'django_redis.client.DefaultClient',90	},91    },92}93REDIS_TIMEOUT=7*24*60*6094CUBES_REDIS_TIMEOUT=60*6095NEVER_REDIS_TIMEOUT=365*24*60*6096LOGIN_URL='/login/'97AUTH_USER_MODEL = 'red.User'98AUTHENTICATION_BACKENDS = ('django.contrib.auth.backends.ModelBackend',)99# Password validation100# https://docs.djangoproject.com/en/1.10/ref/settings/#auth-password-validators101AUTH_PASSWORD_VALIDATORS = [102    {103        'NAME': 'django.contrib.auth.password_validation.UserAttributeSimilarityValidator',104    },105    {106        'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator',107    },108    {109        'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator',110    },111    {112        'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator',113    },114]115# Internationalization116# https://docs.djangoproject.com/en/1.10/topics/i18n/117LANGUAGE_CODE = 'en-us'118TIME_ZONE = 'UTC'119USE_I18N = True120USE_L10N = True121USE_TZ = True122# Static files (CSS, JavaScript, Images)123# https://docs.djangoproject.com/en/1.10/howto/static-files/124STATIC_URL = '/static/'125MEDIA_ROOT ='media/'...

restrictedopd.py

Source:restrictedopd.py

...11    obj_df.columns = ['id', 'name', 'number', 'occurrences']12    obj_df = obj_df.astype({'number': 'int32'})13    return obj_df14def extract_distributions(data):15    log = section_logger(1)16    log('Extracting distributions ')17    raw_data = data[['image_id', 'name']].reset_index()18    raw_data.columns = ['class', 'image_id', 'name']19    raw_data = raw_data.astype({'image_id': 'int32'})20    frequencies = raw_data.pivot_table(21        index='image_id',22        columns='name',23        values='class',24        aggfunc='count',25        fill_value=0.0)26    frequencies['sum'] = frequencies.sum(1)27    frequencies[frequencies.columns.difference(['image_id', 'sum'])] = \28        frequencies[frequencies.columns.difference(['image_id', 'sum'])].div(frequencies["sum"], axis=0)29    img_objs = extract_global_objs(frequencies)30    obj_df = extract_objects(data)31    return img_objs, obj_df32def generate_vgopd_from_restrictedvg(output_path, input_path, top_objects, perc):33    section = section_logger()34    section('Loading RestrictedVG Dataset')35    restricted_definitions = load_dataframe(input_path)36    section('Creating distributions')37    image_df, obj_df = extract_distributions(restricted_definitions)38    section('Saving Raw DataFrame')39    save_raw_data(output_path, obj_df, image_df)40    section('Filtering objects')41    data_df = filter_top_objects(image_df, obj_df, top_objects)42    splits = split_distributions(data_df, perc)43    section('Saving final distribution')44    save_distributions(output_path, splits)45if __name__== "__main__":46    generate_vgopd_from_restrictedvg('/home/dani/Documentos/Proyectos/Doctorado/Datasets/RestrictedOPD/1000C',47                                     '/home/dani/Documentos/Proyectos/Doctorado/Datasets/restrictedGenome', 1000, 0.10)

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