def copy_system_colormaps(self):
"""Verify system colormaps are copied to user's folder"""
colormaps_folder = os.path.join(pathfinder.app_path(), 'colormaps')
colormaps = os.listdir(colormaps_folder)
self.remove_system_files(colormaps, pathfinder.colormaps_path())
self.model.copy_system_colormaps()
for cmap in colormaps:
installed_cmap = os.path.join(pathfinder.colormaps_path(), cmap)
self.assertTrue(os.path.exists(installed_cmap))
def copy_system_colormaps(cls):
"""Copies matplotlib colormaps that ship with the application to the user's colormaps folder."""
colormaps_folder = os.path.join(pathfinder.app_path(), 'colormaps')
colormaps = os.listdir(colormaps_folder)
for colormap_file in colormaps:
shutil.copy(os.path.join(colormaps_folder, colormap_file),
pathfinder.colormaps_path())
def check_user_path(self):
"""Verify user data folders were created"""
data_folders = [pathfinder.user_path(), pathfinder.data_path(),
pathfinder.thumbnails_path(), pathfinder.gates_path(),
pathfinder.plugins_path(), pathfinder.podmodels_path(),
pathfinder.colormaps_path(), pathfinder.batchoutput_path()]
self.model.check_user_path()
for folder in data_folders:
self.assertTrue(os.path.exists(folder))
def check_user_path(self):
"""Verify user data folders were created"""
data_folders = [pathfinder.user_path(), pathfinder.data_path(),
pathfinder.thumbnails_path(), pathfinder.gates_path(),
pathfinder.plugins_path(), pathfinder.podmodels_path(),
pathfinder.adamodels_path(), pathfinder.colormaps_path(),
pathfinder.batchoutput_path()]
self.model.check_user_path()
for folder in data_folders:
self.assertTrue(os.path.exists(folder))
def get_user_colormaps(self, cmap_fldr=pathfinder.colormaps_path()):
"""Returns a list of user-defined colormaps in the specified folder (defaults to
standard colormaps folder if not specified)."""
user_colormaps = []
for root, dirs, files in os.walk(cmap_fldr):
for name in files:
with open(os.path.join(root, name), "r") as fidin:
cmap_dict = json.load(fidin)
user_colormaps.append(cmap_dict.get('name', name))
return user_colormaps
def get_user_colormaps(self, cmap_fldr=pathfinder.colormaps_path()):
"""Returns a list of user-defined colormaps in the specified folder (defaults to
standard colormaps folder if not specified)."""
user_colormaps = []
for root, dirs, files in os.walk(cmap_fldr):
for name in files:
with open(os.path.join(root, name), "r") as fidin:
cmap_dict = json.load(fidin)
user_colormaps.append(cmap_dict.get('name', name))
return user_colormaps
def test_save_colormap(self):
"""Verify saving a colormap"""
shipped_colormaps_folder = os.path.join(pathfinder.app_path(), 'colormaps')
shipped_colormaps = os.listdir(shipped_colormaps_folder)
for shipped_colormap in shipped_colormaps:
shipped_colormap_file = os.path.join(shipped_colormaps_folder, shipped_colormap)
with open(shipped_colormap_file, "r") as fidin:
cmap_dict = json.load(fidin)
self.model.save_colormap(cmap_dict)
cmap_file = os.path.join(pathfinder.colormaps_path(), cmap_dict['name'])
self.assertTrue(os.path.exists(cmap_file))
def get_cmap(self, cmap_name, cmap_folder=pathfinder.colormaps_path()):
"""Returns the matplotlib colormap of the specified name - if not found in the predefined
colormaps, searches for the colormap in the specified folder (defaults to standard colormaps
folder if not specified)."""
user_colormaps = self.get_user_colormaps(cmap_folder)
system_colormaps = self.get_system_colormaps()
if cmap_name in system_colormaps:
return cm.get_cmap(cmap_name)
elif cmap_name in user_colormaps:
cmap_file = os.path.join(cmap_folder, cmap_name)
cmap = self.load_colormap(cmap_file)
return cmap
def get_cmap(self, cmap_name, usercmaps_folder=pathfinder.colormaps_path()):
"""Returns a matplotlib colormap of specified name cmap_name, searching the predefined
matplotlib colormaps first. If not found, attempts to search for JSON file cmap_name in
specified folder (defaults to app's colormaps folder) for valid colormap. Returns None
if no valid colormap could be found."""
system_colormaps = [m for m in cm.datad]
if cmap_name in system_colormaps:
return cm.get_cmap(cmap_name)
for root, dirs, files in os.walk(usercmaps_folder):
if cmap_name in files:
return self.create_cmap(self.get_cmap_dict(os.path.join(root, cmap_name)))
return None
def get_cmap(self, cmap_name, cmap_folder=pathfinder.colormaps_path()):
"""Returns the matplotlib colormap of the specified name - if not found in the predefined
colormaps, searches for the colormap in the specified folder (defaults to standard colormaps
folder if not specified)."""
user_colormaps = self.get_user_colormaps(cmap_folder)
system_colormaps = self.get_system_colormaps()
if cmap_name in system_colormaps:
return cm.get_cmap(cmap_name)
elif cmap_name in user_colormaps:
cmap_file = os.path.join(cmap_folder, cmap_name)
cmap = self.load_colormap(cmap_file)
return cmap
def save_colormap(self, cmap_dict):
"""Saves a properly-formatted colormap dict as a new user-defined colormap.
keys:values
'name': name of the new colormap (str)
'type': one of 'linear' or 'list'. A linear colormap creates a gradient by linearly interpolating between
colors; a list colormap uses the supplied colors as the colormap without interpolation.
'colors': a list of tuples that define the colors. Each color tuple is a three-element RGB (R,G,B) where
each element is between 0 and 1.
"""
cmap_fname = os.path.join(pathfinder.colormaps_path(), cmap_dict['name'])
with open(cmap_fname, "w") as fidout:
json.dump(cmap_dict, fidout)
def save_colormap(self, cmap_dict):
"""Saves a properly-formatted colormap dict as a new user-defined colormap.
keys:values
'name': name of the new colormap (str)
'type': one of 'linear' or 'list'. A linear colormap creates a gradient by linearly interpolating between
colors; a list colormap uses the supplied colors as the colormap without interpolation.
'colors': a list of tuples that define the colors. Each color tuple is a three-element RGB (R,G,B) where
each element is between 0 and 1.
"""
cmap_fname = os.path.join(pathfinder.colormaps_path(),
cmap_dict['name'])
with open(cmap_fname, "w") as fidout:
json.dump(cmap_dict, fidout)
def test_save_colormap(self):
"""Verify saving a colormap"""
shipped_colormaps_folder = os.path.join(pathfinder.app_path(),
'colormaps')
shipped_colormaps = os.listdir(shipped_colormaps_folder)
for shipped_colormap in shipped_colormaps:
shipped_colormap_file = os.path.join(shipped_colormaps_folder,
shipped_colormap)
with open(shipped_colormap_file, "r") as fidin:
cmap_dict = json.load(fidin)
self.model.save_colormap(cmap_dict)
cmap_file = os.path.join(pathfinder.colormaps_path(),
cmap_dict['name'])
self.assertTrue(os.path.exists(cmap_file))
def check_user_path(cls):
"""Verify that user data folders exist. Creates
any missing folders."""
user_folder = pathfinder.user_path()
data_folder = pathfinder.data_path()
thumbnail_folder = pathfinder.thumbnails_path()
plugins_folder = pathfinder.plugins_path()
podmodels_folder = pathfinder.podmodels_path()
adamodels_folder = pathfinder.adamodels_path()
gates_folder = pathfinder.gates_path()
colormaps_folder = pathfinder.colormaps_path()
batch_folder = pathfinder.batchoutput_path()
for fldr in (user_folder, data_folder, thumbnail_folder, plugins_folder, podmodels_folder, gates_folder,
adamodels_folder, colormaps_folder, batch_folder):
if not os.path.exists(fldr):
os.makedirs(fldr)
def check_user_path(cls):
"""Verify that user data folders exist. Creates
any missing folders."""
user_folder = pathfinder.user_path()
data_folder = pathfinder.data_path()
thumbnail_folder = pathfinder.thumbnails_path()
plugins_folder = pathfinder.plugins_path()
podmodels_folder = pathfinder.podmodels_path()
gates_folder = pathfinder.gates_path()
colormaps_folder = pathfinder.colormaps_path()
batch_folder = pathfinder.batchoutput_path()
for fldr in (user_folder, data_folder, thumbnail_folder,
plugins_folder, podmodels_folder, gates_folder,
colormaps_folder, batch_folder):
if not os.path.exists(fldr):
os.makedirs(fldr)
def deleted_user_path():
"""Utility function to delete empty folders in the user data folders,
used to verify that MainModel will recreate missing folders as required.
Returns a list of folders successfully deleted or None if no folders
were deleted."""
data_folders = [pathfinder.user_path(), pathfinder.data_path(), pathfinder.thumbnails_path(),
pathfinder.plugins_path(), pathfinder.colormaps_path()]
deleted_folders = []
for folder in data_folders:
exists_and_empty = os.path.exists(folder) and os.listdir(folder) == []
if exists_and_empty:
try:
os.rmdir(folder)
deleted_folders.append(folder)
except WindowsError: # folder in use (Explorer, cmd, etc.)
pass
if deleted_folders:
return deleted_folders
return None
def deleted_user_path():
"""Utility function to delete empty folders in the user data folders,
used to verify that MainModel will recreate missing folders as required.
Returns a list of folders successfully deleted or None if no folders
were deleted."""
data_folders = [pathfinder.user_path(), pathfinder.data_path(), pathfinder.thumbnails_path(),
pathfinder.plugins_path(), pathfinder.podmodels_path(), pathfinder.adamodels_path(),
pathfinder.colormaps_path()]
deleted_folders = []
for folder in data_folders:
exists_and_empty = os.path.exists(folder) and os.listdir(folder) == []
if exists_and_empty:
try:
os.rmdir(folder)
deleted_folders.append(folder)
except WindowsError: # folder in use (Explorer, cmd, etc.)
pass
if deleted_folders:
return deleted_folders
return None
def test_colormaps_path(self):
"""Verify returning correct path to colormaps"""
colormaps_path = os.path.join(self.user_path, "colormaps")
self.assertEqual(colormaps_path, pathfinder.colormaps_path())
def test_colormaps_path(self):
"""Verify returning correct path to colormaps"""
colormaps_path = os.path.join(self.user_path, "colormaps")
self.assertEqual(colormaps_path, pathfinder.colormaps_path())
def copy_system_colormaps(cls):
"""Copies matplotlib colormaps that ship with the application to the user's colormaps folder."""
colormaps_folder = os.path.join(pathfinder.app_path(), 'colormaps')
colormaps = os.listdir(colormaps_folder)
for colormap_file in colormaps:
shutil.copy(os.path.join(colormaps_folder, colormap_file), pathfinder.colormaps_path())