1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267
|
# fmt: off
"""
Module for managing viewers
View plugins can be registered through the entrypoint system in with the
following in a module, such as a `viewer.py` file:
```python3
VIEWER_ENTRYPOINT = ExternalViewer(
desc="Visualization using <my package>",
module="my_package.viewer"
)
```
Where module `my_package.viewer` contains a `view_my_viewer` function taking
and `ase.Atoms` object as the first argument, and also `**kwargs`.
Then ones needs to register an entry point in `pyproject.toml` with
```toml
[project.entry-points."ase.visualize"]
my_viewer = "my_package.viewer:VIEWER_ENTRYPOINT"
```
After this, call to `ase.visualize.view(atoms, viewer='my_viewer')` will be
forwarded to `my_package.viewer.view_my_viewer` function.
"""
import pickle
import subprocess
import sys
import tempfile
import warnings
from contextlib import contextmanager
from importlib import import_module
from importlib.metadata import entry_points
from io import BytesIO
from pathlib import Path
from ase.io import write
from ase.io.formats import ioformats
from ase.utils.plugins import ExternalViewer
class UnknownViewerError(Exception):
"""The view tyep is unknown"""
class AbstractViewer:
def view(self, *args, **kwargss):
raise NotImplementedError
class PyViewer(AbstractViewer):
def __init__(self, name: str, desc: str, module_name: str):
"""
Instantiate an viewer
"""
self.name = name
self.desc = desc
self.module_name = module_name
def _viewfunc(self):
"""Return the function used for viewing the atoms"""
return getattr(self.module, "view_" + self.name, None)
@property
def module(self):
try:
return import_module(self.module_name)
except ImportError as err:
raise UnknownViewerError(
f"Viewer not recognized: {self.name}. Error: {err}"
) from err
def view(self, atoms, *args, **kwargs):
return self._viewfunc()(atoms, *args, **kwargs)
class CLIViewer(AbstractViewer):
"""Generic viewer for"""
def __init__(self, name, fmt, argv):
self.name = name
self.fmt = fmt
self.argv = argv
@property
def ioformat(self):
return ioformats[self.fmt]
@contextmanager
def mktemp(self, atoms, data=None):
ioformat = self.ioformat
suffix = "." + ioformat.extensions[0]
if ioformat.isbinary:
mode = "wb"
else:
mode = "w"
with tempfile.TemporaryDirectory(prefix="ase-view-") as dirname:
# We use a tempdir rather than a tempfile because it's
# less hassle to handle the cleanup on Windows (files
# cannot be open on multiple processes).
path = Path(dirname) / f"atoms{suffix}"
with path.open(mode) as fd:
if data is None:
write(fd, atoms, format=self.fmt)
else:
write(fd, atoms, format=self.fmt, data=data)
yield path
def view_blocking(self, atoms, data=None):
with self.mktemp(atoms, data) as path:
subprocess.check_call(self.argv + [str(path)])
def view(
self,
atoms,
data=None,
repeat=None,
**kwargs,
):
"""Spawn a new process in which to open the viewer."""
if repeat is not None:
atoms = atoms.repeat(repeat)
proc = subprocess.Popen(
[sys.executable, "-m", "ase.visualize.viewers"],
stdin=subprocess.PIPE
)
pickle.dump((self, atoms, data), proc.stdin)
proc.stdin.close()
return proc
VIEWERS = {}
def _pipe_to_ase_gui(atoms, repeat, **kwargs):
buf = BytesIO()
write(buf, atoms, format="traj")
args = [sys.executable, "-m", "ase", "gui", "-"]
if repeat:
args.append("--repeat={},{},{}".format(*repeat))
proc = subprocess.Popen(args, stdin=subprocess.PIPE)
proc.stdin.write(buf.getvalue())
proc.stdin.close()
return proc
def define_viewer(
name, desc, *, module=None, cli=False, fmt=None, argv=None, external=False
):
if not external:
if module is None:
module = name
module = "ase.visualize." + module
if cli:
fmt = CLIViewer(name, fmt, argv)
else:
if name == "ase":
# Special case if the viewer is named `ase` then we use
# the _pipe_to_ase_gui as the viewer method
fmt = PyViewer(name, desc, module_name=None)
fmt.view = _pipe_to_ase_gui
else:
fmt = PyViewer(name, desc, module_name=module)
VIEWERS[name] = fmt
return fmt
def define_external_viewer(entry_point):
"""Define external viewer"""
viewer_def = entry_point.load()
if entry_point.name in VIEWERS:
raise ValueError(f"Format {entry_point.name} already defined")
if not isinstance(viewer_def, ExternalViewer):
raise TypeError(
"Wrong type for registering external IO formats "
f"in format {entry_point.name}, expected "
"ExternalViewer"
)
define_viewer(entry_point.name, **viewer_def._asdict(),
external=True)
def register_external_viewer_formats(group):
if hasattr(entry_points(), "select"):
viewer_entry_points = entry_points().select(group=group)
else:
viewer_entry_points = entry_points().get(group, ())
for entry_point in viewer_entry_points:
try:
define_external_viewer(entry_point)
except Exception as exc:
warnings.warn(
"Failed to register external "
f"Viewer {entry_point.name}: {exc}"
)
define_viewer("ase", "View atoms using ase gui.")
define_viewer("ngl", "View atoms using nglview.")
define_viewer("mlab", "View atoms using matplotlib.")
define_viewer("sage", "View atoms using sage.")
define_viewer("x3d", "View atoms using x3d.")
# CLI viweers that are internally supported
define_viewer(
"avogadro", "View atoms using avogradro.", cli=True, fmt="cube",
argv=["avogadro"]
)
define_viewer(
"ase_gui_cli", "View atoms using ase gui.", cli=True, fmt="traj",
argv=[sys.executable, '-m', 'ase.gui'],
)
define_viewer(
"gopenmol",
"View atoms using gopenmol.",
cli=True,
fmt="extxyz",
argv=["runGOpenMol"],
)
define_viewer(
"rasmol",
"View atoms using rasmol.",
cli=True,
fmt="proteindatabank",
argv=["rasmol", "-pdb"],
)
define_viewer("vmd", "View atoms using vmd.", cli=True, fmt="cube",
argv=["vmd"])
define_viewer(
"xmakemol",
"View atoms using xmakemol.",
cli=True,
fmt="extxyz",
argv=["xmakemol", "-f"],
)
register_external_viewer_formats("ase.visualize")
CLI_VIEWERS = {key: value for key, value in VIEWERS.items()
if isinstance(value, CLIViewer)}
PY_VIEWERS = {key: value for key, value in VIEWERS.items()
if isinstance(value, PyViewer)}
def cli_main():
"""
This is mainly to facilitate launching CLI viewer in a separate python
process
"""
cli_viewer, atoms, data = pickle.load(sys.stdin.buffer)
cli_viewer.view_blocking(atoms, data)
if __name__ == "__main__":
cli_main()
|