diff --git a/python/cable_cell_io.cpp b/python/cable_cell_io.cpp
index 5191c47b730b96466e9d7f7c7b38060071eab1d7..335371df227ae9d80235a006bc5a9e742612a6aa 100644
--- a/python/cable_cell_io.cpp
+++ b/python/cable_cell_io.cpp
@@ -2,6 +2,7 @@
#include <pybind11/stl.h>
#include <fstream>
+#include <iostream>
#include <iomanip>
#include <arbor/cable_cell.hpp>
@@ -19,14 +20,10 @@ namespace pyarb {
namespace py = pybind11;
arborio::cable_cell_component load_component(py::object fn) {
- const auto fname = util::to_path(fn);
- std::ifstream fid{fname};
- if (!fid.good()) {
- throw arb::file_not_found_error(fname);
- }
- auto component = arborio::parse_component(fid);
+ auto contents = util::read_file_or_buffer(fn);
+ auto component = arborio::parse_component(contents);
if (!component) {
- throw pyarb_error("Error while trying to load component from \"" + fname + "\": " + component.error().what());
+ throw pyarb_error(std::string{"Error while trying to load component: "} + component.error().what());
}
return component.value();
};
diff --git a/python/morphology.cpp b/python/morphology.cpp
index 8f4293ca13dba4128ee1f66e9ff5fc32c3ec8f54..ba238754a000fc6227f73ecb67eae1b502f99d05 100644
--- a/python/morphology.cpp
+++ b/python/morphology.cpp
@@ -252,22 +252,17 @@ void register_morphology(py::module& m) {
// Wraps calls to C++ functions arborio::parse_swc() and arborio::load_swc_arbor().
m.def("load_swc_arbor",
[](py::object fn) {
- const auto fname = util::to_path(fn);
- std::ifstream fid{fname};
- if (!fid.good()) {
- throw arb::file_not_found_error(fname);
- }
try {
- auto data = arborio::parse_swc(fid);
- check_trailing(fid, fname);
+ auto contents = util::read_file_or_buffer(fn);
+ auto data = arborio::parse_swc(contents);
return arborio::load_swc_arbor(data);
}
catch (arborio::swc_error& e) {
// Try to produce helpful error messages for SWC parsing errors.
- throw pyarb_error(util::pprintf("error parsing {}: {}", fname, e.what()));
+ throw pyarb_error(util::pprintf("Arbor SWC: parse error: {}", e.what()));
}
},
- "filename"_a,
+ "filename_or_stream"_a,
"Generate a morphology from an SWC file following the rules prescribed by Arbor.\n"
"Specifically:\n"
"* Single-segment somas are disallowed.\n"
@@ -278,23 +273,18 @@ void register_morphology(py::module& m) {
m.def("load_swc_neuron",
[](py::object fn) {
- const auto fname = util::to_path(fn);
- std::ifstream fid{fname};
- if (!fid.good()) {
- throw arb::file_not_found_error(fname);
- }
try {
- auto data = arborio::parse_swc(fid);
- check_trailing(fid, fname);
+ auto contents = util::read_file_or_buffer(fn);
+ auto data = arborio::parse_swc(contents);
return arborio::load_swc_neuron(data);
}
catch (arborio::swc_error& e) {
// Try to produce helpful error messages for SWC parsing errors.
throw pyarb_error(
- util::pprintf("NEURON SWC: error parsing {}: {}", fname, e.what()));
+ util::pprintf("NEURON SWC: parse error: {}", e.what()));
}
},
- "filename"_a,
+ "filename_or_stream"_a,
"Generate a morphology from an SWC file following the rules prescribed by NEURON.\n"
"See the documentation https://docs.arbor-sim.org/en/latest/fileformat/swc.html\n"
"for a detailed description of the interpretation.");
@@ -343,9 +333,10 @@ void register_morphology(py::module& m) {
"The four canonical regions are labeled 'soma', 'axon', 'dend' and 'apic'.");
m.def("load_asc",
- [](std::string fname) {
+ [](py::object fn) {
try {
- return arborio::load_asc(fname);
+ auto contents = util::read_file_or_buffer(fn);
+ return arborio::load_asc(contents);
}
catch (std::exception& e) {
// Try to produce helpful error messages for SWC parsing errors.
@@ -387,21 +378,16 @@ void register_morphology(py::module& m) {
// constructors
.def(py::init(
[](py::object fn) {
- const auto fname = util::to_path(fn);
- std::ifstream fid{fname};
- if (!fid.good()) {
- throw arb::file_not_found_error(fname);
- }
try {
- std::string string_data((std::istreambuf_iterator<char>(fid)),
- std::istreambuf_iterator<char>());
- return arborio::neuroml(string_data);
+ auto contents = util::read_file_or_buffer(fn);
+ return arborio::neuroml(contents);
}
catch (arborio::neuroml_exception& e) {
// Try to produce helpful error messages for NeuroML parsing errors.
- throw pyarb_error(util::pprintf("NeuroML error processing file {}: {}", fname, e.what()));
+ throw pyarb_error(util::pprintf("NeuroML error: {}", e.what()));
}
- }))
+ }),
+ "Construct NML morphology from filename or stream.")
.def("cell_ids",
[](const arborio::neuroml& nml) {
try {
diff --git a/python/test/unit/test_io.py b/python/test/unit/test_io.py
new file mode 100644
index 0000000000000000000000000000000000000000..b3eda93b99f6ca19d937c951f08882538376215a
--- /dev/null
+++ b/python/test/unit/test_io.py
@@ -0,0 +1,93 @@
+import unittest
+
+import arbor as A
+
+from pathlib import Path
+from tempfile import TemporaryDirectory as TD
+from io import StringIO
+
+acc = """(arbor-component
+ (meta-data
+ (version "0.1-dev"))
+ (cable-cell
+ (morphology
+ (branch 0 -1
+ (segment 0
+ (point -3.000000 0.000000 0.000000 3.000000)
+ (point 3.000000 0.000000 0.000000 3.000000)
+ 1)))
+ (label-dict
+ (region-def "soma"
+ (tag 1))
+ (locset-def "mid"
+ (location 0 0.5)))
+ (decor
+ (default
+ (membrane-potential -40.000000))
+ (default
+ (ion-internal-concentration "ca" 0.000050))
+ (default
+ (ion-external-concentration "ca" 2.000000))
+ (default
+ (ion-reversal-potential "ca" 132.457934))
+ (default
+ (ion-internal-concentration "k" 54.400000))
+ (default
+ (ion-external-concentration "k" 2.500000))
+ (default
+ (ion-reversal-potential "k" -77.000000))
+ (default
+ (ion-internal-concentration "na" 10.000000))
+ (default
+ (ion-external-concentration "na" 140.000000))
+ (default
+ (ion-reversal-potential "na" 50.000000))
+ (paint
+ (tag 1)
+ (density
+ (mechanism "default::hh"
+ ("gnabar" 0.120000)
+ ("el" -54.300000)
+ ("q10" 0.000000)
+ ("gl" 0.000300)
+ ("gkbar" 0.036000))))
+ (place
+ (location 0 0.5)
+ (current-clamp
+ (envelope
+ (10.000000 0.800000)
+ (12.000000 0.000000))
+ 0.000000 0.000000)
+ "I Clamp 0"))))
+"""
+
+
+class TestAccIo(unittest.TestCase):
+ def test_stringio(self):
+ sio = StringIO(acc)
+ A.load_component(sio)
+
+ def test_fileio(self):
+ fn = "test.acc"
+ with TD() as tmp:
+ tmp = Path(tmp)
+ with open(tmp / fn, "w") as fd:
+ fd.write(acc)
+ with open(tmp / fn) as fd:
+ A.load_component(fd)
+
+ def test_nameio(self):
+ fn = "test.acc"
+ with TD() as tmp:
+ tmp = Path(tmp)
+ with open(tmp / fn, "w") as fd:
+ fd.write(acc)
+ A.load_component(str(tmp / fn))
+
+ def test_pathio(self):
+ fn = "test.acc"
+ with TD() as tmp:
+ tmp = Path(tmp)
+ with open(tmp / fn, "w") as fd:
+ fd.write(acc)
+ A.load_component(tmp / fn)
diff --git a/python/util.hpp b/python/util.hpp
index fe1b6b07d100b7e46fe41b82029aa51282344b33..4a096f6f0a319409f97d02355b2f5f160b098fbc 100644
--- a/python/util.hpp
+++ b/python/util.hpp
@@ -1,8 +1,11 @@
#pragma once
+#include <fstream>
+
#include <pybind11/pybind11.h>
#include "strprintf.hpp"
+#include "error.hpp"
namespace pyarb {
namespace util {
@@ -19,9 +22,29 @@ std::string to_path(py::object fn) {
return std::string{py::str(fn)};
}
throw std::runtime_error(
- util::strprintf("Cannot convert objects of type '{}' to a path-like.",
+ util::pprintf("Cannot convert objects of type {} to a path-like.",
std::string{py::str(fn.get_type())}));
}
+inline
+std::string read_file_or_buffer(py::object fn) {
+ if (py::hasattr(fn, "read")) {
+ return py::str(fn.attr("read")(-1));
+ } else {
+ const auto fname = util::to_path(fn);
+ std::ifstream fid{fname};
+ if (!fid.good()) {
+ throw arb::file_not_found_error(fname);
+ }
+ std::string result;
+ fid.seekg(0, fid.end);
+ auto sz = fid.tellg();
+ fid.seekg(0, fid.beg);
+ result.resize(sz);
+ fid.read(result.data(), sz);
+ return result;
+ }
+}
+
}
}