def __init__(self, view):
self.view = view
self.dc = None
self.clustering = None
self.lap_descriptors = None
self.cluster_class = None
self.node_class = None
self.sample_ids = []
self.sample_data = {}
self.distance = None
self.dist_rels = [
"diam_dist", "axis_dist", "dice_dist", "dice_rim_dist"
]
# self.sample_data = {sample_id: [obj_id, descriptors], ...}
# descriptors = {
# profile = {Profile_Geometry, Profile_Rim, Profile_Bottom, Profile_Radius, Profile_Radius_Point, Profile_Rim_Point, Profile_Bottom_Point, Arc_Geometry: []}
# details = {target_id: {Detail_Geometry, Detail_Closed, Detail_Filled}, ...}
# inflections = {target_id: {Inflection_Geometry, Inflection_Dashed}, ...}
# breaks = {target_id: {Break_Geometry}, ...}
# }
self._has_distance = False
self._last_changed = -1
Store.__init__(self, parent=self.view)
self.clustering = Clustering(self)
self.broadcast_timer = QtCore.QTimer()
def set_up(self):
self.setMinimumWidth(600)
self.setModal(True)
self.layout = QtWidgets.QVBoxLayout()
self.setLayout(self.layout)
self.form_layout = QtWidgets.QFormLayout()
self.form = QtWidgets.QWidget()
self.form.setLayout(self.form_layout)
self.layout.addWidget(self.form)
self.temp_store = Store()
self.db = self.temp_store.datasources.DB()
self.dbrel = self.temp_store.datasources.DBRel()
self.ds = None
connstrings = []
for row in self.view.menu.get_recent(
): # [[url], [identifier, connstr], ...]
if len(row) == 2:
connstrings.append(row[1])
self.connstr = QtWidgets.QComboBox()
if connstrings:
self.connstr.addItems(connstrings)
self.connstr.setEditable(True)
self.connstr.currentTextChanged.connect(self.on_connstr_changed)
self.identifier = QtWidgets.QListWidget()
self.form_layout.addRow("Connect string:", self.connstr)
self.form_layout.addRow("Identifier:", self.identifier)
if connstrings:
self.on_connstr_changed(connstrings[0])
def __init__(self, model, view, parent):
self.model = model
self.view = view
self.parent = parent
self._connstr_prev = None
self._schemas = defaultdict(lambda: defaultdict(
list)) # {server: {db_name: [schema, ...], ...}, ...}
self._identifiers = []
DModule.__init__(self)
QtWidgets.QFrame.__init__(self, parent)
self.form = QtWidgets.QWidget()
self.form.setLayout(QtWidgets.QFormLayout())
self.setLayout(QtWidgets.QVBoxLayout())
self.layout().setContentsMargins(10, 10, 10, 10)
self.server_combo = QtWidgets.QComboBox()
self.server_combo.setEditable(True)
self.db_name_combo = QtWidgets.QComboBox()
self.db_name_combo.setEditable(True)
self.schema_name_combo = QtWidgets.QComboBox()
self.schema_name_combo.setEditable(True)
self.schema_name_combo.setCurrentText("public")
self.user_edit = QtWidgets.QLineEdit("")
self.user_edit.textChanged.connect(self.update)
self.pass_edit = QtWidgets.QLineEdit("")
self.pass_edit.setEchoMode(QtWidgets.QLineEdit.Password)
self.pass_edit.textChanged.connect(self.update)
self.identifier_combo = QtWidgets.QComboBox()
self.identifier_combo.setEditable(True)
self.local_folder_edit = QtWidgets.QLineEdit("")
self.local_folder_edit.textChanged.connect(self.on_local_folder_edit)
self.local_folder_edit._edited = False
self.lf_browse_button = QtWidgets.QPushButton("Browse...")
self.lf_browse_button.clicked.connect(self.on_lf_browse)
lf_container = QtWidgets.QWidget()
lf_container.setLayout(QtWidgets.QHBoxLayout())
lf_container.layout().setContentsMargins(0, 0, 0, 0)
lf_container.layout().addWidget(self.local_folder_edit)
lf_container.layout().addWidget(self.lf_browse_button)
self.temp_store = Store()
self.db = self.temp_store.datasources.DB()
servers = []
logins = []
names = {} # {server: [name, ...], ...}
for row in self.view.menu.get_recent(
): # [[url], [identifier, connstr], ...]
if len(row) == 2:
server, name = row[1].split("/")[-2:]
schema = "public"
if "?" in name:
name, schema = name.split("?")
schema = schema.split("%3D")[-1]
user, server = server.split("@")
user, password = user.split(":")
if server not in names:
names[server] = []
if name not in names[server]:
names[server].append(name)
if schema not in self._schemas[server][name]:
self._schemas[server][name].append(schema)
if server not in servers:
servers.append(server)
logins.append([user, password])
self.server_combo.addItem("")
for i in range(len(servers)):
self.server_combo.addItem(servers[i], [servers[i]] + logins[i] +
[names[servers[i]]])
self.server_combo.editTextChanged.connect(self.on_server_changed)
self.db_name_combo.editTextChanged.connect(self.update)
self.schema_name_combo.editTextChanged.connect(self.update)
self.identifier_combo.editTextChanged.connect(
self.on_identifier_changed)
self.connect_button = QtWidgets.QPushButton(
self.parent.connect_caption())
self.connect_button.clicked.connect(self.on_connect)
self.form.layout().addRow("Server[:port]:", self.server_combo)
self.form.layout().addRow("Database:", self.db_name_combo)
self.form.layout().addRow("Schema:", self.schema_name_combo)
self.form.layout().addRow("Username:"******"Password:"******"Identifier:", self.identifier_combo)
self.form.layout().addRow("Local Folder:", lf_container)
self.layout().addWidget(self.form)
self.layout().addWidget(self.connect_button,
alignment=QtCore.Qt.AlignCenter)
self.layout().addStretch()
self.update()
class DataSourceDB(DModule, QtWidgets.QFrame):
def __init__(self, model, view, parent):
self.model = model
self.view = view
self.parent = parent
self._connstr_prev = None
self._schemas = defaultdict(lambda: defaultdict(
list)) # {server: {db_name: [schema, ...], ...}, ...}
self._identifiers = []
DModule.__init__(self)
QtWidgets.QFrame.__init__(self, parent)
self.form = QtWidgets.QWidget()
self.form.setLayout(QtWidgets.QFormLayout())
self.setLayout(QtWidgets.QVBoxLayout())
self.layout().setContentsMargins(10, 10, 10, 10)
self.server_combo = QtWidgets.QComboBox()
self.server_combo.setEditable(True)
self.db_name_combo = QtWidgets.QComboBox()
self.db_name_combo.setEditable(True)
self.schema_name_combo = QtWidgets.QComboBox()
self.schema_name_combo.setEditable(True)
self.schema_name_combo.setCurrentText("public")
self.user_edit = QtWidgets.QLineEdit("")
self.user_edit.textChanged.connect(self.update)
self.pass_edit = QtWidgets.QLineEdit("")
self.pass_edit.setEchoMode(QtWidgets.QLineEdit.Password)
self.pass_edit.textChanged.connect(self.update)
self.identifier_combo = QtWidgets.QComboBox()
self.identifier_combo.setEditable(True)
self.local_folder_edit = QtWidgets.QLineEdit("")
self.local_folder_edit.textChanged.connect(self.on_local_folder_edit)
self.local_folder_edit._edited = False
self.lf_browse_button = QtWidgets.QPushButton("Browse...")
self.lf_browse_button.clicked.connect(self.on_lf_browse)
lf_container = QtWidgets.QWidget()
lf_container.setLayout(QtWidgets.QHBoxLayout())
lf_container.layout().setContentsMargins(0, 0, 0, 0)
lf_container.layout().addWidget(self.local_folder_edit)
lf_container.layout().addWidget(self.lf_browse_button)
self.temp_store = Store()
self.db = self.temp_store.datasources.DB()
servers = []
logins = []
names = {} # {server: [name, ...], ...}
for row in self.view.menu.get_recent(
): # [[url], [identifier, connstr], ...]
if len(row) == 2:
server, name = row[1].split("/")[-2:]
schema = "public"
if "?" in name:
name, schema = name.split("?")
schema = schema.split("%3D")[-1]
user, server = server.split("@")
user, password = user.split(":")
if server not in names:
names[server] = []
if name not in names[server]:
names[server].append(name)
if schema not in self._schemas[server][name]:
self._schemas[server][name].append(schema)
if server not in servers:
servers.append(server)
logins.append([user, password])
self.server_combo.addItem("")
for i in range(len(servers)):
self.server_combo.addItem(servers[i], [servers[i]] + logins[i] +
[names[servers[i]]])
self.server_combo.editTextChanged.connect(self.on_server_changed)
self.db_name_combo.editTextChanged.connect(self.update)
self.schema_name_combo.editTextChanged.connect(self.update)
self.identifier_combo.editTextChanged.connect(
self.on_identifier_changed)
self.connect_button = QtWidgets.QPushButton(
self.parent.connect_caption())
self.connect_button.clicked.connect(self.on_connect)
self.form.layout().addRow("Server[:port]:", self.server_combo)
self.form.layout().addRow("Database:", self.db_name_combo)
self.form.layout().addRow("Schema:", self.schema_name_combo)
self.form.layout().addRow("Username:"******"Password:"******"Identifier:", self.identifier_combo)
self.form.layout().addRow("Local Folder:", lf_container)
self.layout().addWidget(self.form)
self.layout().addWidget(self.connect_button,
alignment=QtCore.Qt.AlignCenter)
self.layout().addStretch()
self.update()
def get_values(self):
server = self.server_combo.currentText().strip()
name = self.db_name_combo.currentText().strip()
schema = self.schema_name_combo.currentText().strip()
user = self.user_edit.text().strip()
password = self.pass_edit.text().strip()
identifier = self.identifier_combo.currentText().strip()
local_folder = self.local_folder_edit.text().strip()
if server and (":" not in server):
server = "%s:5432" % (server)
return server, name, schema, user, password, identifier, local_folder
def load_schemas(self):
server, name, curr_schema, user, password, identifier, _ = self.get_values(
)
if not self._schemas[server][name]:
connstr = "postgres://%s:%s@%s/%s" % (user, password, server, name)
conn = None
try:
conn = psycopg2.connect(connstr)
except:
pass
if conn is not None:
cursor = conn.cursor()
cursor.execute(
"SELECT schema_name FROM information_schema.schemata")
self._schemas[server][name] = natsorted(
[row[0] for row in cursor.fetchall()])
if "public" not in self._schemas[server][name]:
self._schemas[server][name].append("public")
self.schema_name_combo.blockSignals(True)
self.schema_name_combo.clear()
self.schema_name_combo.addItems(self._schemas[server][name])
if curr_schema:
self.schema_name_combo.setCurrentText(curr_schema)
self.schema_name_combo.blockSignals(False)
def load_identifiers(self):
self.identifier_combo.blockSignals(True)
server, name, schema, user, password, identifier, _ = self.get_values()
do_not_load = (self._schemas[server][name]
and (schema not in self._schemas[server][name]))
connstr = "postgres://%s:%s@%s/%s?options=-csearch_path%%3D%s" % (
user, password, server, name, schema)
if connstr != self._connstr_prev:
self._identifiers = []
self.identifier_combo.clear()
if (not do_not_load) and ("" not in [
server, name, schema, user, password
]):
if self.db.set_connstr(connstr):
self._identifiers = self.db.get_identifiers()
if self._identifiers:
self.identifier_combo.addItems(self._identifiers)
self.local_folder_edit._edited = False
if identifier:
self.identifier_combo.setCurrentText(identifier)
if (not identifier) and self._identifiers:
identifier = self._identifiers[0]
if (not self.local_folder_edit._edited) and (identifier
in self._identifiers):
local_folder = self.db.get_local_folder(identifier)
self.local_folder_edit.blockSignals(True)
self.local_folder_edit.setText(local_folder)
self.local_folder_edit.blockSignals(False)
self._connstr_prev = connstr
self.identifier_combo.blockSignals(False)
def update(self, *args):
self.load_schemas()
self.load_identifiers()
server, name, schema, user, password, identifier, local_folder = self.get_values(
)
is_valid = False
if as_identifier(
identifier,
default_base="http://localhost/deposit") in self._identifiers:
self.connect_button.setText(self.parent.connect_caption())
is_valid = True
elif self.parent.creating_enabled():
self.connect_button.setText("Create")
is_valid = True
if not local_folder:
is_valid = False
self.connect_button.setEnabled(
is_valid and
(""
not in [server, name, user, password, identifier, local_folder]))
def create_db(self, connstr, identifier):
if not self.parent.creating_enabled():
return False
ds = self.temp_store.datasources.DB(identifier=identifier,
connstr=connstr)
cursor, _ = ds.connect(create_schema=True)
if cursor:
return ds.save()
return False
def on_local_folder_edit(self):
self.local_folder_edit._edited = True
self.update()
def on_server_changed(self):
data = self.server_combo.currentData()
server = self.server_combo.currentText().strip()
if data:
server, user, password, names = data
_, curr_name, curr_schema, curr_user, curr_password, _, _ = self.get_values(
)
if not (curr_user or curr_password):
curr_user, curr_password = user, password
self.user_edit.blockSignals(True)
self.pass_edit.blockSignals(True)
self.user_edit.setText(user)
self.pass_edit.setText(password)
self.user_edit.blockSignals(False)
self.pass_edit.blockSignals(False)
if names:
self.db_name_combo.blockSignals(True)
self.db_name_combo.clear()
self.db_name_combo.addItems(names)
if curr_name:
self.db_name_combo.setCurrentText(curr_name)
self.db_name_combo.blockSignals(False)
self.update()
def on_identifier_changed(self):
self.local_folder_edit._edited = False
self.update()
def on_lf_browse(self):
path = QtWidgets.QFileDialog.getExistingDirectory(
self, caption="Select Local Folder")
if path:
self.local_folder_edit._edited = True
self.local_folder_edit.setText(
os.path.normpath(os.path.abspath(path)))
def on_connect(self):
server, name, schema, user, password, identifier, local_folder = self.get_values(
)
if "" in [server, name, schema, user, password, identifier]:
return
connstr = "postgres://%s:%s@%s/%s?options=-csearch_path%%3D%s" % (
user, password, server, name, schema)
identifier = as_identifier(identifier,
default_base="http://localhost/deposit")
if not os.path.isdir(local_folder):
os.mkdir(local_folder)
if identifier in self._identifiers:
if self.temp_store.get_datasource(identifier, connstr):
self.parent.on_connect(identifier,
connstr,
local_folder,
created=False)
else:
QtWidgets.QMessageBox.critical(
self, "Error", "Could not connect to database.")
else:
if self.create_db(connstr, identifier):
self.parent.on_connect(identifier,
connstr,
local_folder,
created=True)
else:
QtWidgets.QMessageBox.critical(self, "Error",
"Could not create database.")
def set_datasource(self, data_source):
self.clear_samples()
Store.set_datasource(self, data_source)
from deposit.store.Store import Store
from lib.fnc_matching import *
store = Store()
store.load("d:\\documents_synced\\CeraMatch\\DEP_kap_typology\\kap_typology.json")
cmax = len(store.classes["Sample"].objects)
cnt = 1
for id in store.classes["Sample"].objects:
print("\r%d/%d " % (cnt, cmax), end = "")
cnt += 1
obj = store.objects[id]
profile = np.array(obj.descriptors["Profile"].label.coords[0])
axis, thickness = profile_axis(profile, rasterize_factor = 10)
axis_length = np.sqrt((np.diff(axis, axis = 0) ** 2).sum(axis = 1)).sum()
obj.add_descriptor("Axis_Length", axis_length)
obj.add_descriptor("Norm_Length", axis_length / thickness)
store.save()