[tag] v0.5.0, update jdata to 0.8, use 1-time init in test

- use defaultdict in brain2mesh
- add pylintrc
- some code clean up based on pylint
- fix mergemesh shallow copy

Author: fangq

.pylintrc

@@ -11,11 +11,14 @@ test:
 build:
 	$(PY) -m build
 
+lint:
+	pylint iso2mesh
+
 report:
 	@echo '====== all imported functions ======'
 	@grep '^\s*[a-z]*,' iso2mesh/__init__.py | sed -e 's/^\s*//g' -e 's/,//g' | sort | uniq -c
 	@echo '====== all tested functions ======'
 	@grep 'def\s*test' test/run_test.py | sed -e 's/\s*def test_//g' -e 's/(self)://g' -e 's/_.*//g' | sort | uniq -c
 
 .DEFAULT_GOAL=all
-.PHONY: all pretty test report
+.PHONY: all pretty test report lint

Makefile

@@ -4,7 +4,7 @@
 
 * **Copyright**: (C) Qianqian Fang (2024-2025) <q.fang at neu.edu>
 * **License**: GNU Public License V3 or later
-* **Version**: 0.4.2
+* **Version**: 0.5.0
 * **URL**: [https://pypi.org/project/iso2mesh/](https://pypi.org/project/iso2mesh/)
 * **Homepage**: [https://iso2mesh.sf.net](https://iso2mesh.sf.net)
 * **Github**: [https://github.com/NeuroJSON/pyiso2mesh](https://github.com/NeuroJSON/pyiso2mesh)
@@ -225,25 +225,25 @@ tracked in https://github.com/NeuroJSON/pyiso2mesh/issues/1
 | ✅ `meshunitsphere.m` | ✅ tested |         | ✅ `loadjson.m`                    | ⭕️ tested |
 | ✅ `meshacylinder.m` | ✅ tested |          | ✅ `savejd.m`                      | ⭕️ tested |
 | ✅ `meshgrid5.m` | ✅ tested |              | ✅ `loadjd.m`                      | ⭕️ tested |
-| ✅ `meshgrid6.m` | ✅ tested |              | ⭕️ `loadmsgpack.m`                | ⭕️ tested |
-| ✅ `latticegrid.m` | ✅ tested |            | ⭕️ `savemsgpack.m`                | ⭕️ tested |
+| ✅ `meshgrid6.m` | ✅ tested |              | ✅ `loadmsgpack.m`                | ⭕️ tested |
+| ✅ `latticegrid.m` | ✅ tested |            | ✅ `savemsgpack.m`                | ⭕️ tested |
 | ✅ `extrudecurve.m` | ⭕️ tested |           | ✅ `savebj.m`                      | ⭕️ tested |
 | ✅ `meshcylinders.m` | ✅ tested |          | ✅ `loadbj.m`                      | ⭕️ tested |
 | > Mesh decomposition and query| |           | ⭕️ `savemphtxt.m`                 | ⭕️ tested |
-| ✅ `finddisconnsurf.m` | ✅ tested |        | ⭕️ `savetetgenele.m`              | ⭕️ tested |
-| ✅ `surfedge.m` | ✅ tested |               | ⭕️ `savetetgennode.m`             | ⭕️ tested |
+| ✅ `finddisconnsurf.m` | ✅ tested |        | ✅ `savetetgenele.m`              | ⭕️ tested |
+| ✅ `surfedge.m` | ✅ tested |               | ✅ `savetetgennode.m`             | ⭕️ tested |
 | ✅ `volface.m` | ✅ tested |                | ⭕️ `saveabaqus.m`                 | ⭕️ tested |
 | ✅ `extractloops.m` | ✅ tested |           | ⭕️ `savenirfast.m`                | ⭕️ tested |
 | ✅ `meshconn.m` | ✅ tested |               | ⭕️ `readnirfast.m`                | ⭕️ tested |
 | ✅ `meshcentroid.m` | ✅ tested |           | ✅ `loadnifti.m`                   | ⭕️ tested |
 | ✅ `nodevolume.m` | ✅ tested |             | ⭕️ `readmptiff.m`                 | ⭕️ tested |
-| ✅ `elemvolume.m` | ✅ tested |             | ⭕️ `loadjsnirf.m`                 | ⭕️ tested |
-| ✅ `neighborelem.m` | ✅ tested |           | ⭕️ `savejsnirf.m`                 | ⭕️ tested |
-| ✅ `layersurf.m` | ⭕️ tested |              | ⭕️ `loadsnirf.m`                  | ⭕️ tested |
-| ✅ `faceneighbors.m` | ✅ tested |          | ⭕️ `savesnirf.m`                  | ⭕️ tested |
+| ✅ `elemvolume.m` | ✅ tested |             | ✅ `loadjsnirf.m`                 | ⭕️ tested |
+| ✅ `neighborelem.m` | ✅ tested |           | ✅ `savejsnirf.m`                 | ⭕️ tested |
+| ✅ `layersurf.m` | ⭕️ tested |              | ✅ `loadsnirf.m`                  | ⭕️ tested |
+| ✅ `faceneighbors.m` | ✅ tested |          | ✅ `savesnirf.m`                  | ⭕️ tested |
 | ✅ `edgeneighbors.m` | ✅ tested |          | ⭕️ `readobjmesh.m`                | ⭕️ tested |
 | ✅ `maxsurf.m` | ⭕️ tested |                | ⭕️ `loadjmesh.m`                  | ⭕️ tested |
-| ✅ `flatsegment.m` | ⭕️ tested |            | ⭕️ `readobjmesh.m`                | ⭕️ tested |
+| ✅ `flatsegment.m` | ⭕️ tested |            | ⭕️ `savejmesh.m`                  | ⭕️ tested |
 | ✅ `orderloopedge.m` | ⭕️ tested |          | > Volumetric image pre-processing | |
 | ✅ `mesheuler.m` | ✅ tested |              | ✅ `volgrow.m`                     | ✅ tested |
 | ✅ `bbxflatsegment.m` | ⭕️ tested |         | ✅ `volshrink.m`                   | ✅ tested |
@@ -274,8 +274,8 @@ tracked in https://github.com/NeuroJSON/pyiso2mesh/issues/1
 | ✅ `getintersecttri.m` | ⭕️ tested |        | ⭕️ `isoctavemesh.m`               | ⭕️ tested |
 | ✅ `delendelem.m` | ⭕️ tested |             | ⭕️ `getvarfrom.m`                 | ⭕️ tested |
 | ✅ `surfreorient.m` | ✅ tested |           | ✅ `raytrace.m`                    | ✅ tested |
-| > Mesh registration | |                     | ⭕️ `linextriangle.m`              | ⭕️ tested |
-| ✅ `proj2mesh.m` | ⭕️ tested |              | ⭕️ `getplanefrom3pt.m`            | ⭕️ tested |
+| > Mesh registration | |                     | ✅ `linextriangle.m`              | ⭕️ tested |
+| ✅ `proj2mesh.m` | ⭕️ tested |              | ✅ `getplanefrom3pt.m`            | ⭕️ tested |
 | ✅ `dist2surf.m` | ⭕️ tested |              | ✅ `getexeext.m`                   | ✅ tested |
 | ✅ `regpt2surf.m` | ⭕️ tested |             | ✅ `fallbackexeext.m`              | ✅ tested |
 | ✅ `affinemap.m` | ⭕️ tested |              | ⭕️ `iso2meshver.m`                | ⭕️ tested |
@@ -289,8 +289,8 @@ tracked in https://github.com/NeuroJSON/pyiso2mesh/issues/1
 | > Mesh resampling and optimization| |       | ⭕️ `orthdisk.m`                   | ⭕️ tested |
 | ✅ `meshresample.m` | ✅ tested |           | ⭕️ `nestbracket2dim.m`            | ⭕️ tested |
 | ✅ `remeshsurf.m` | ✅ tested |             | ✅ `memmapstream.m`                | ⭕️ tested |
-| ✅ `smoothsurf.m` | ✅ tested |             | ⭕️ `aos2soa.m`                    | ⭕️ tested |
-| ✅ `sortmesh.m` | ⭕️ tested |               | ⭕️ `soa2aos.m`                    | ⭕️ tested |
+| ✅ `smoothsurf.m` | ✅ tested |             | ✅ `aos2soa.m`                    | ⭕️ tested |
+| ✅ `sortmesh.m` | ⭕️ tested |               | ✅ `soa2aos.m`                    | ⭕️ tested |
 | ✅ `mergemesh.m` | ✅ tested |              | > Brain2mesh toolbox              | |
 | ✅ `meshrefine.m` | ✅ tested |             | ✅ `brain2mesh.m`                  | ⭕️ tested |
 | ✅ `mergesurf.m` | ⭕️ tested |              | ✅ `brain1020.m`                   | ⭕️ tested |

README.md

@@ -1,14 +1,74 @@
 """pyiso2mesh - Iso2Mesh for Python
 """
 
+from jdata import (
+    loadjson,
+    savejson,
+    loadbj,
+    savebj,
+    loadjd,
+    savejd,
+    jdataencode,
+    jdatadecode,
+    loadurl,
+    jsoncache,
+    jdlink,
+    jsonpath,
+    nii2jnii,
+    jnii2nii,
+    loadnifti,
+    loadjnifti,
+    savenifti,
+    savejnifti,
+    nifticreate,
+    jnifticreate,
+    memmapstream,
+    niiheader2jnii,
+    niicodemap,
+    niiformat,
+    savebnii,
+    savejnii,
+    loadh5,
+    saveh5,
+    regrouph5,
+    aos2soa,
+    soa2aos,
+    jsnirfcreate,
+    snirfcreate,
+    loadjsnirf,
+    loadsnirf,
+    savejsnirf,
+    savesnirf,
+    snirfdecode,
+    zlibencode,
+    zlibdecode,
+    gzipencode,
+    gzipdecode,
+    lzmaencode,
+    lzmadecode,
+    lz4encode,
+    lz4decode,
+    base64encode,
+    base64decode,
+    neuroj,
+    neurojgui,
+    load_csv_tsv,
+    loadcsv,
+    loadtsv,
+    save_csv_tsv,
+    loadmsgpack,
+    savemsgpack,
+    loadubjson,
+    saveubjson,
+)
+
 from .geometry import (
     meshgrid5,
     meshgrid6,
     latticegrid,
     meshabox,
     meshacylinder,
     meshcylinders,
-    meshcylinders,
     meshanellip,
     meshunitsphere,
     meshasphere,
@@ -122,7 +182,6 @@
     removeisolatedsurf,
     surfaceclean,
     removeedgefaces,
-    getintersecttri,
     delendelem,
     surfreorient,
     sortmesh,
@@ -178,9 +237,7 @@
     thinbinvol,
 )
 
-from jdata import *
-
-__version__ = "0.4.2"
+__version__ = "0.5.0"
 __all__ = [
     "advancefront",
     "barycentricgrid",
@@ -205,7 +262,6 @@
     "flatsegment",
     "getexeext",
     "getintersecttri",
-    "getintersecttri",
     "highordertet",
     "innersurf",
     "insurface",
@@ -357,5 +413,29 @@
     "jdlink",
     "jsoncache",
     "loadurl",
+    "regrouph5",
+    "aos2soa",
+    "soa2aos",
+    "jsnirfcreate",
+    "snirfcreate",
+    "loadjsnirf",
+    "loadsnirf",
+    "savejsnirf",
+    "savesnirf",
+    "snirfdecode",
+    "neuroj",
+    "neurojgui",
+    "load_csv_tsv",
+    "loadcsv",
+    "loadtsv",
+    "save_csv_tsv",
+    "loadmsgpack",
+    "savemsgpack",
+    "loadubjson",
+    "saveubjson",
+    "savebnii",
+    "savejnii",
+    "loadh5",
+    "saveh5",
 ]
 __license__ = """GNU General Public License v3 and later"""

iso2mesh/__init__.py

@@ -16,7 +16,6 @@
 ##====================================================================================
 
 import numpy as np
-import sys
 from iso2mesh.core import v2s, s2m
 from iso2mesh.modify import (
     removeisolatednode,
@@ -42,9 +41,8 @@
 from iso2mesh.plot import plotmesh
 
 from typing import Tuple, Dict, Union, Optional, List
-import matplotlib.pyplot as plt
 import warnings
-from collections import OrderedDict
+from collections import defaultdict
 
 ##====================================================================================
 ## implementations
@@ -130,8 +128,10 @@ def brain2mesh(seg, **cfg):
         return
 
     # Default density and adaptiveness parameters
-    density = {"wm": 2, "gm": 2, "csf": 5, "skull": 4, "scalp": 8}
-    adaptiveness = {"wm": 1, "gm": 1, "csf": 1, "skull": 1, "scalp": 1}
+    density = defaultdict(
+        lambda: 20, {"wm": 2, "gm": 2, "csf": 5, "skull": 4, "scalp": 8}
+    )
+    adaptiveness = defaultdict(lambda: 1)
 
     # Parse configuration
     radbound = cfg.get("radbound", density)
@@ -147,7 +147,7 @@ def brain2mesh(seg, **cfg):
     surfonly = cfg.get("surfonly", 0)
     marginsize = cfg.get("marginsize", 4)
 
-    segname = list(density.keys())
+    segname = list(radbound.keys())
 
     # Convert seg to dict format if needed
     if isinstance(seg, dict):
@@ -1387,7 +1387,9 @@ def brain1020(
     # At this point, initpoints contains {nz, iz, lpa, rpa, cz0}
     # Plot the head mesh
     if showplot:
-        hh = plotmesh(node, face, alpha=0, color="wheat", linewidth=0.1)
+        hh = plotmesh(
+            node, face, alpha=0.5, color="wheat", edgecolor="k", linewidth=0.1
+        )
         ax = hh["ax"][0]
         ax.set_xlabel("X")
         ax.set_ylabel("Y")
@@ -1915,37 +1917,3 @@ def tpm2label(
         return vol, names
     else:
         return vol
-
-
-def orderfields_python(struct_dict, order: List[str]):
-    """
-    Python equivalent of MATLAB's orderfields function
-
-    Reorders dictionary fields according to specified order.
-
-    Parameters:
-    -----------
-    struct_dict : dict
-        Dictionary to reorder
-    order : list
-        List specifying the desired field order
-
-    Returns:
-    --------
-    ordered_dict : dict
-        Dictionary with fields reordered according to order
-    """
-
-    ordered_dict = OrderedDict()
-
-    # First add fields in the specified order
-    for field_name in order:
-        if field_name in struct_dict:
-            ordered_dict[field_name] = struct_dict[field_name]
-
-    # Then add any remaining fields that weren't in the order list
-    for field_name, field_value in struct_dict.items():
-        if field_name not in ordered_dict:
-            ordered_dict[field_name] = field_value
-
-    return ordered_dict

iso2mesh/brain2mesh.py

@@ -30,11 +30,11 @@
 ## dependent libraries
 ##====================================================================================
 
-import numpy as np
 import os
 import re
 import sys
 import subprocess
+import numpy as np
 from iso2mesh.trait import (
     surfinterior,
     surfseeds,
@@ -48,7 +48,14 @@
     maxsurf,
     ismember_rows,
 )
-from iso2mesh.utils import *
+from iso2mesh.utils import (
+    getexeext,
+    deletemeshfile,
+    mwpath,
+    mcpath,
+    fallbackexeext,
+    jsonopt,
+)
 from iso2mesh.io import (
     saveoff,
     readoff,

iso2mesh/core.py

@@ -25,11 +25,10 @@
 ##====================================================================================
 
 import numpy as np
-import sys
 from itertools import permutations, combinations
 from iso2mesh.core import surf2mesh, vol2restrictedtri
 from iso2mesh.trait import meshreorient, volface, surfedge, nodesurfnorm
-from iso2mesh.utils import *
+from iso2mesh.utils import rotatevec3d
 from iso2mesh.modify import removeisolatednode, meshcheckrepair
 
 # _________________________________________________________________________________________________________

iso2mesh/geometry.py

@@ -195,7 +195,7 @@ def polylinelen(node, p0=None, p1=None, pmid=None):
     p1 -= 1
     pmid -= 1
 
-    if p0 < pmid and pmid < p1:
+    if p0 < pmid < p1:
         inputreversed = 0
         node = node[range(p0, p1 + 1), :]
     elif p0 < pmid and p1 < pmid:
@@ -206,7 +206,7 @@ def polylinelen(node, p0=None, p1=None, pmid=None):
         node = node[idx_range, :]
         if not inputreversed:
             node = np.flipud(node)
-    elif p0 > pmid and pmid > p1:
+    elif p0 > pmid > p1:
         inputreversed = 1
         node = node[range(p0, p1 - 1, -1), :]
     elif p0 > pmid and p1 > pmid: