11254817533

Committed 09 Oct 2024 12:20PM UTC coverage: 77.697% (+0.08%) from 77.615%

Build # 11254817533

Build Type

Pull #476

github

Committed by

mgeplf

Commit Message

Merge remote-tracking branch 'origin/master' into efficient-swc-build

Pull Request Pull Request #476: Efficient swc build

Run Details

286 of 321 new or added lines in 10 files covered. (89.1%)

9 existing lines in 4 files now uncovered.

2125 of 2735 relevant lines covered (77.7%)

901.01 hits per line

Source File
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90.91

/src/mut/writer_asc.cpp

/* Copyright (c) 2013-2023, EPFL/Blue Brain Project
 *
 * SPDX-License-Identifier: Apache-2.0
 */
#include <fstream>
#include <iomanip>  // std::fixed, std::setw, std::setprecision

#include <morphio/mut/mitochondria.h>
#include <morphio/mut/morphology.h>
#include <morphio/mut/section.h>
#include <morphio/mut/writers.h>
#include <morphio/version.h>
#include <morphio/warning_handling.h>

#include "../error_message_generation.h"
#include "../shared_utils.hpp"
#include "writer_utils.h"

namespace {
void write_asc_points(std::ofstream& myfile,
                      const morphio::Points& points,
                      const std::vector<morphio::floatType>& diameters,
                      size_t indentLevel) {
    for (unsigned int i = 0; i < points.size(); ++i) {
        myfile << std::fixed << std::setprecision(morphio::FLOAT_PRECISION_PRINT)
               << std::string(indentLevel, ' ') << '(' << points[i][0] << ' ' << points[i][1] << ' '
               << points[i][2] << ' ' << diameters[i] << ")\n";
    }
}

void write_asc_section(std::ofstream& myfile,
                       const std::shared_ptr<morphio::mut::Section>& section,
                       size_t indentLevel) {
    const std::string indent(indentLevel, ' ');
    write_asc_points(myfile, section->points(), section->diameters(), indentLevel);

    if (!section->children().empty()) {
        auto children = section->children();
        size_t nChildren = children.size();
        for (unsigned int i = 0; i < nChildren; ++i) {
            myfile << indent << (i == 0 ? "(\n" : "|\n");
            write_asc_section(myfile, children[i], indentLevel + 2);
        }
        myfile << indent << ")\n";
    }
}
}  // namespace

namespace morphio {
namespace mut {
namespace writer {

void asc(const Morphology& morph,
         const std::string& filename,
         std::shared_ptr<morphio::WarningHandler> handler) {
    if (details::emptyMorphology(morph, handler)) {
        throw morphio::WriterError(morphio::details::ErrorMessages().ERROR_EMPTY_MORPHOLOGY());
    }

    details::validateContourSoma(morph, handler);
    details::checkSomaHasSameNumberPointsDiameters(*morph.soma());
    details::validateHasNoMitochondria(morph, handler);
    details::validateHasNoPerimeterData(morph);
    details::validateRootPointsHaveTwoOrMorePoints(morph);

    std::ofstream myfile(filename);

    const std::shared_ptr<Soma>& soma = morph.soma();
    if (!soma->points().empty()) {
        myfile << "(\"CellBody\"\n  (Color Red)\n  (CellBody)\n";
        write_asc_points(myfile, soma->points(), soma->diameters(), 2);
        myfile << ")\n\n";
    }

    for (const std::shared_ptr<Section>& section : morph.rootSections()) {
        const auto type = section->type();
        if (type == SECTION_AXON) {
            myfile << "( (Color Cyan)\n  (Axon)\n";
        } else if (type == SECTION_DENDRITE) {
            myfile << "( (Color Red)\n  (Dendrite)\n";
        } else if (type == SECTION_APICAL_DENDRITE) {
            myfile << "( (Color Red)\n  (Apical)\n";
        } else {
            throw WriterError(
                morphio::details::ErrorMessages().ERROR_UNSUPPORTED_SECTION_TYPE(type));
        }
        write_asc_section(myfile, section, 2);
        myfile << ")\n\n";
    }

    myfile << "; " << details::version_string() << '\n';
}
}  // end namespace writer
}  // end namespace mut
}  // end namespace morphio

1	/* Copyright (c) 2013-2023, EPFL/Blue Brain Project
2	*
3	* SPDX-License-Identifier: Apache-2.0
4	*/
5	#include <fstream>
6	#include <iomanip> // std::fixed, std::setw, std::setprecision
7
8	#include <morphio/mut/mitochondria.h>
9	#include <morphio/mut/morphology.h>
10	#include <morphio/mut/section.h>
11	#include <morphio/mut/writers.h>
12	#include <morphio/version.h>
13	#include <morphio/warning_handling.h>
14
15	#include "../error_message_generation.h"
16	#include "../shared_utils.hpp"
17	#include "writer_utils.h"
18
19	namespace {
20	void write_asc_points(std::ofstream& myfile,	14✔
21	const morphio::Points& points,
22	const std::vector<morphio::floatType>& diameters,
23	size_t indentLevel) {
24	for (unsigned int i = 0; i < points.size(); ++i) {	46✔
25	myfile << std::fixed << std::setprecision(morphio::FLOAT_PRECISION_PRINT)	32✔
26	<< std::string(indentLevel, ' ') << '(' << points[i][0] << ' ' << points[i][1] << ' '	64✔
27	<< points[i][2] << ' ' << diameters[i] << ")\n";	32✔
28	}
29	}	14✔
30
31	void write_asc_section(std::ofstream& myfile,	12✔
32	const std::shared_ptr<morphio::mut::Section>& section,
33	size_t indentLevel) {
34	const std::string indent(indentLevel, ' ');	24✔
35	write_asc_points(myfile, section->points(), section->diameters(), indentLevel);	12✔
36
37	if (!section->children().empty()) {	12✔
38	auto children = section->children();	8✔
39	size_t nChildren = children.size();	4✔
40	for (unsigned int i = 0; i < nChildren; ++i) {	12✔
41	myfile << indent << (i == 0 ? "(\n" : "\|\n");	8✔
42	write_asc_section(myfile, children[i], indentLevel + 2);	8✔
43	}
44	myfile << indent << ")\n";	4✔
45	}
46	}	12✔
47	} // namespace
48
49	namespace morphio {
50	namespace mut {
51	namespace writer {
52
53	void asc(const Morphology& morph,	2✔
54	const std::string& filename,
55	std::shared_ptr<morphio::WarningHandler> handler) {
56	if (details::emptyMorphology(morph, handler)) {	2✔
NEW 57	throw morphio::WriterError(morphio::details::ErrorMessages().ERROR_EMPTY_MORPHOLOGY());	×
58	}
59
60	details::validateContourSoma(morph, handler);	2✔
61	details::checkSomaHasSameNumberPointsDiameters(*morph.soma());	2✔
62	details::validateHasNoMitochondria(morph, handler);	2✔
63	details::validateHasNoPerimeterData(morph);	2✔
64	details::validateRootPointsHaveTwoOrMorePoints(morph);	2✔
65
66	std::ofstream myfile(filename);	2✔
67
68	const std::shared_ptr<Soma>& soma = morph.soma();	2✔
69	if (!soma->points().empty()) {	2✔
70	myfile << "(\"CellBody\"\n (Color Red)\n (CellBody)\n";	2✔
71	write_asc_points(myfile, soma->points(), soma->diameters(), 2);	2✔
72	myfile << ")\n\n";	2✔
73	}
74
75	for (const std::shared_ptr<Section>& section : morph.rootSections()) {	6✔
76	const auto type = section->type();	4✔
77	if (type == SECTION_AXON) {	4✔
78	myfile << "( (Color Cyan)\n (Axon)\n";	2✔
79	} else if (type == SECTION_DENDRITE) {	2✔
80	myfile << "( (Color Red)\n (Dendrite)\n";	2✔
81	} else if (type == SECTION_APICAL_DENDRITE) {	×
82	myfile << "( (Color Red)\n (Apical)\n";	×
83	} else {
84	throw WriterError(
NEW 85	morphio::details::ErrorMessages().ERROR_UNSUPPORTED_SECTION_TYPE(type));	×
86	}
87	write_asc_section(myfile, section, 2);	4✔
88	myfile << ")\n\n";	4✔
89	}
90
91	myfile << "; " << details::version_string() << '\n';	2✔
92	}	2✔
93	} // end namespace writer
94	} // end namespace mut
95	} // end namespace morphio

BlueBrain / MorphIO / 11254817533

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