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the tria_io private subpackage had some unexpected error handling #50

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merged 2 commits into from
Jan 9, 2024
Merged

the tria_io private subpackage had some unexpected error handling #50

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31c34a0
the tria_io private subpackage had some unexpected error handling
dkuegler Jan 8, 2024
dccd831
fix black code formatting
dkuegler Jan 8, 2024
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105 changes: 47 additions & 58 deletions lapy/_tria_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@
Should be called via the TriaMesh member functions.
"""

from logging import getLogger

import numpy as np


Expand All @@ -19,9 +21,7 @@ def read_fssurf(filename):
TriaMesh
Loaded triangle mesh.
"""
verbose = 1
if verbose > 0:
print("--> FS Surf format ... ")
getLogger(__name__).debug("--> FS Surf format ... ")
try:
# here we use our copy to also support surfaces from dev (and maybe v7*?)
# these have an empty line and mess up Nibabel
Expand All @@ -31,7 +31,7 @@ def read_fssurf(filename):
surf = read_geometry(filename, read_metadata=True)
except IOError:
print("[file not found or not readable]\n")
return
raise
from . import TriaMesh

return TriaMesh(surf[0], surf[1], fsinfo=surf[2])
Expand All @@ -50,21 +50,20 @@ def read_off(filename):
TriaMesh
Loaded triangle mesh.
"""
verbose = 1
if verbose > 0:
print("--> OFF format ... ")
getLogger(__name__).debug("--> OFF format ... ")
try:
f = open(filename, "r")
except IOError:
print("[file not found or not readable]\n")
return
raise
line = f.readline()
while line[0] == "#":
line = f.readline()
if not line.startswith("OFF"):
print("[OFF keyword not found] --> FAILED\n")
msg = "[OFF keyword not found] --> FAILED\n"
print(msg)
f.close()
return
raise IOError(msg)
# expect tria and vertex sizes after OFF line:
line = f.readline()
larr = line.split()
Expand All @@ -82,12 +81,13 @@ def read_off(filename):
# max0 = np.amax(t[:, 0])
# print(" max: {}".format(max0))
if np.amax(t[:, 0]) != 3:
print("[no triangle data] --> FAILED\n")
msg = "[no triangle data] --> FAILED\n"
print(msg)
f.close()
return
raise IOError(msg)
t = t[:, 1:]
f.close()
print(" --> DONE ( V: " + str(v.shape[0]) + " , T: " + str(t.shape[0]) + " )\n")
getLogger(__name__).info(f" --> DONE ( V: {v.shape[0]} , T: {t.shape[0]} )\n")
from . import TriaMesh

return TriaMesh(v, t)
Expand All @@ -106,14 +106,12 @@ def read_vtk(filename):
TriaMesh
Loaded triangle mesh.
"""
verbose = 1
if verbose > 0:
print("--> VTK format ... ")
getLogger(__name__).debug("--> VTK format ... ")
try:
f = open(filename, "r")
except IOError:
print("[file not found or not readable]\n")
return
raise
# skip comments
line = f.readline()
while line[0] == "#":
Expand All @@ -125,29 +123,27 @@ def read_vtk(filename):
# print line
count = count + 1
if not line.startswith("ASCII"):
print("[ASCII keyword not found] --> FAILED\n")
return
msg = "[ASCII keyword not found] --> FAILED\n"
print(msg)
raise IOError(msg)
# expect Dataset Polydata line after ASCII:
line = f.readline()
if not line.startswith("DATASET POLYDATA") and not line.startswith(
"DATASET UNSTRUCTURED_GRID"
):
print(
"[read: "
+ line
+ " expected DATASET POLYDATA or DATASET UNSTRUCTURED_GRID] --> FAILED\n"
msg = (
f"[read: {line} expected DATASET POLYDATA or DATASET UNSTRUCTURED_GRID] "
f"--> FAILED\n"
)
return
print(msg)
raise IOError(msg)
# read number of points
line = f.readline()
larr = line.split()
if larr[0] != "POINTS" or (larr[2] != "float" and larr[2] != "double"):
print(
"[read: "
+ line
+ " expected POINTS # float or POINTS # double ] --> FAILED\n"
)
return
msg = f"[read: {line} expected POINTS # float or POINTS # double ] --> FAILED\n"
print(msg)
raise IOError(msg)
pnum = int(larr[1])
# read points as chunk
v = np.fromfile(f, "float32", 3 * pnum, " ")
Expand All @@ -160,17 +156,15 @@ def read_vtk(filename):
ttnum = int(larr[2])
npt = float(ttnum) / tnum
if npt != 4.0:
print(
"[having: "
+ str(npt)
+ " data per tria, expected trias 3+1] --> FAILED\n"
)
return
msg = f"[having: {npt} data per tria, expected trias 3+1] --> FAILED\n"
print(msg)
raise IOError(msg)
t = np.fromfile(f, "int", ttnum, " ")
t.shape = (tnum, 4)
if t[tnum - 1][0] != 3:
print("[can only read triangles] --> FAILED\n")
return
msg = "[can only read triangles] --> FAILED\n"
print(msg)
raise IOError(msg)
t = np.delete(t, 0, 1)
elif larr[0] == "TRIANGLE_STRIPS":
tnum = int(larr[1])
Expand All @@ -179,12 +173,14 @@ def read_vtk(filename):
for i in range(tnum):
larr = f.readline().split()
if len(larr) == 0:
print("[error reading triangle strip (i)] --> FAILED\n")
return
msg = "[error reading triangle strip (i)] --> FAILED\n"
print(msg)
raise IOError(msg)
n = int(larr[0])
if len(larr) != n + 1:
print("[error reading triangle strip (ii)] --> FAILED\n")
return
msg = "[error reading triangle strip (ii)] --> FAILED\n"
print(msg)
raise IOError(msg)
# create triangles from strip
# note that larr tria info starts at index 1
for ii in range(2, n):
Expand All @@ -195,10 +191,11 @@ def read_vtk(filename):
tt.append(tria)
t = np.array(tt)
else:
print("[read: " + line + " expected POLYGONS or TRIANGLE_STRIPS] --> FAILED\n")
return
msg = f"[read: {line} expected POLYGONS or TRIANGLE_STRIPS] --> FAILED\n"
print(msg)
raise IOError(msg)
f.close()
print(" --> DONE ( V: " + str(v.shape[0]) + " , T: " + str(t.shape[0]) + " )\n")
getLogger(__name__).info(f" --> DONE ( V: {v.shape[0]} , T: {t.shape[0]} )\n")
from . import TriaMesh

return TriaMesh(v, t)
Expand Down Expand Up @@ -281,15 +278,13 @@ def read_gmsh(filename):
}
_meshio_to_gmsh_type = {v: k for k, v in _gmsh_to_meshio_type.items()} # noqa: F841

verbose = 1
if verbose > 0:
print("--> GMSH format ... ")
getLogger(__name__).debug("--> GMSH format ... ")

try:
f = open(filename, "r")
except IOError:
print("[file not found or not readable]\n")
return
raise

# Initialize the data optional data fields
points = []
Expand Down Expand Up @@ -483,7 +478,7 @@ def write_vtk(tria, filename):
f = open(filename, "w")
except IOError:
print("[File " + filename + " not writable]")
return
raise
# check data structure
# ...
# Write
Expand All @@ -495,13 +490,7 @@ def write_vtk(tria, filename):
for i in range(np.shape(tria.v)[0]):
f.write(" ".join(map(str, tria.v[i, :])))
f.write("\n")
f.write(
"POLYGONS "
+ str(np.shape(tria.t)[0])
+ " "
+ str(4 * np.shape(tria.t)[0])
+ "\n"
)
f.write(f"POLYGONS {np.shape(tria.t)[0]} {4 * np.shape(tria.t)[0]}\n")
for i in range(np.shape(tria.t)[0]):
f.write(" ".join(map(str, np.append(3, tria.t[i, :]))))
f.write("\n")
Expand All @@ -525,4 +514,4 @@ def write_fssurf(tria, filename):
write_geometry(filename, tria.v, tria.t, volume_info=tria.fsinfo)
except IOError:
print("[File " + filename + " not writable]")
return
raise
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