No .type_choice(std::vector<std::string>) #3379
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| Original file line number | Diff line number | Diff line change |
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@@ -16,6 +16,7 @@ | |
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| #include "adapter/regrid.h" | ||
| #include "algo/copy.h" | ||
| #include "app.h" | ||
| #include "command.h" | ||
| #include "enum.h" | ||
| #include "filter/resize.h" | ||
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@@ -131,9 +132,9 @@ void usage() { | |
| + Argument ("factor").type_sequence_float() | ||
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| + Option ("interp", std::string("set the interpolation method to use when reslicing") | ||
| + " (choices: " + MR::Enum::join<MR::Interp::interp_type>() + ";" | ||
| " default: " + MR::Enum::lowercase_name(default_interp) + ").") | ||
| + Argument ("method").type_choice<MR::Interp::interp_type>() | ||
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| + Option ("oversample", | ||
| "set the amount of over-sampling (in the target space) to perform when regridding." | ||
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@@ -221,8 +222,7 @@ void run() { | |
| regrid_filter.set_out_of_bounds_value(out_of_bounds_value); | ||
| size_t resize_option_count = 0; | ||
| size_t template_option_count = 0; | ||
| const MR::Interp::interp_type interp = get_option_choice<MR::Interp::interp_type>("interp", default_interp); | ||
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There was a problem hiding this comment. warning: no header providing "MR::App::get_option_choice" is directly included [misc-include-cleaner] const MR::Interp::interp_type interp = get_option_choice<MR::Interp::interp_type>("interp", default_interp);
^ |
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| // over-sampling | ||
| std::vector<uint32_t> oversample = Adapter::AutoOverSample; | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -16,6 +16,7 @@ | |
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| #include "algo/loop.h" | ||
| #include "algo/threaded_loop.h" | ||
| #include "app.h" | ||
| #include "command.h" | ||
| #include "enum.h" | ||
| #include "image.h" | ||
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@@ -199,9 +200,9 @@ void usage() { | |
| + Argument ("iteration method").type_choice<space_t>() | ||
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| + Option ("interp", std::string("set the interpolation method to use when reslicing") + | ||
| " (choices: " + MR::Enum::join<MR::Interp::interp_type>() + "." | ||
| " Default: " + MR::Enum::lowercase_name(default_interp) + ").") | ||
| + Argument ("method").type_choice<MR::Interp::interp_type>() | ||
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| + Option ("metric", | ||
| "define the dissimilarity metric used to calculate the cost." | ||
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@@ -231,8 +232,7 @@ using MaskType = Image<bool>; | |
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| void run() { | ||
| const space_t space = get_option_choice<space_t>("space", default_space); | ||
| const MR::Interp::interp_type interp = get_option_choice<MR::Interp::interp_type>("interp", default_interp); | ||
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There was a problem hiding this comment. warning: no header providing "MR::App::get_option_choice" is directly included [misc-include-cleaner] const MR::Interp::interp_type interp = get_option_choice<MR::Interp::interp_type>("interp", default_interp);
^ |
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| MetricType metric_type = MetricType::MeanSquared; | ||
| const MetricChoice metric_choice = get_option_choice<MetricChoice>("metric", MetricChoice::DIFF); | ||
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@@ -17,6 +17,7 @@ | |
| #include <filesystem> | ||
| #include <optional> | ||
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| #include "app.h" | ||
| #include "command.h" | ||
| #include "dwi/directions/predefined.h" | ||
| #include "dwi/directions/validate.h" | ||
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@@ -402,12 +403,14 @@ void run() { | |
| if (!opt.empty()) { | ||
| if (init_rigid_matrix_set) | ||
| throw Exception("options -rigid_init_matrix and -rigid_init_translation are mutually exclusive"); | ||
| Registration::set_init_translation_model_from_option( | ||
| rigid_registration, MR::Enum::from_name<Registration::init_translation_t>(opt[0][0])); | ||
| } | ||
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| opt = get_options("rigid_init_rotation"); | ||
| if (!opt.empty()) | ||
| Registration::set_init_rotation_model_from_option(rigid_registration, | ||
| MR::Enum::from_name<Registration::init_rotation_t>(opt[0][0])); | ||
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| opt = get_options("rigid_scale"); | ||
| if (!opt.empty()) { | ||
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@@ -430,20 +433,8 @@ void run() { | |
| rigid_registration.set_max_iter(parse_ints<uint32_t>(opt[0][0])); | ||
| } | ||
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| const Registration::LinearMetricType rigid_metric = | ||
| get_option_choice<Registration::LinearMetricType>("rigid_metric", Registration::Diff); | ||
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There was a problem hiding this comment. warning: no header providing "MR::App::get_option_choice" is directly included [misc-include-cleaner] get_option_choice<Registration::LinearMetricType>("rigid_metric", Registration::Diff);
^ |
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| if (rigid_metric == Registration::NCC) | ||
| throw Exception("TODO: cross correlation metric not yet implemented"); | ||
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@@ -453,21 +444,7 @@ void run() { | |
| if (!opt.empty()) { | ||
| if (rigid_metric != Registration::Diff) | ||
| throw Exception("rigid_metric.diff.estimator set but cost function is not diff."); | ||
| rigid_estimator = MR::Enum::from_name<Registration::LinearRobustMetricEstimatorType>(opt[0][0]); | ||
| } | ||
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| opt = get_options("rigid_lmax"); | ||
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@@ -534,14 +511,16 @@ void run() { | |
| if (!opt.empty()) { | ||
| if (init_affine_matrix_set) | ||
| throw Exception("options -affine_init_matrix and -affine_init_translation are mutually exclusive"); | ||
| Registration::set_init_translation_model_from_option( | ||
| affine_registration, MR::Enum::from_name<Registration::init_translation_t>(opt[0][0])); | ||
| } | ||
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| opt = get_options("affine_init_rotation"); | ||
| if (!opt.empty()) { | ||
| if (init_affine_matrix_set) | ||
| throw Exception("options -affine_init_matrix and -affine_init_rotation are mutually exclusive"); | ||
| Registration::set_init_rotation_model_from_option(affine_registration, | ||
| MR::Enum::from_name<Registration::init_rotation_t>(opt[0][0])); | ||
| } | ||
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| opt = get_options("affine_scale"); | ||
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@@ -558,20 +537,8 @@ void run() { | |
| affine_registration.set_loop_density(parse_floats(opt[0][0])); | ||
| } | ||
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| const Registration::LinearMetricType affine_metric = | ||
| get_option_choice<Registration::LinearMetricType>("affine_metric", Registration::Diff); | ||
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| if (affine_metric == Registration::NCC) | ||
| throw Exception("TODO cross correlation metric not yet implemented"); | ||
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@@ -581,22 +548,7 @@ void run() { | |
| if (!opt.empty()) { | ||
| if (affine_metric != Registration::Diff) | ||
| throw Exception("affine_metric.diff.estimator set but cost function is not diff."); | ||
| affine_estimator = MR::Enum::from_name<Registration::LinearRobustMetricEstimatorType>(opt[0][0]); | ||
| } | ||
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| opt = get_options("affine_niter"); | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -15,9 +15,11 @@ | |
| */ | ||
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| #include <iomanip> | ||
| #include <vector> | ||
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| #include "command.h" | ||
| #include "datatype.h" | ||
| #include "enum.h" | ||
| #include "image.h" | ||
| #include "image_helpers.h" | ||
| #include "memory.h" | ||
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@@ -108,10 +110,11 @@ void run() { | |
| check_dimensions(mask, header, 0, 3); | ||
| } | ||
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| std::vector<Stats::field_t> fields; | ||
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There was a problem hiding this comment. warning: no header providing "std::vector" is directly included [misc-include-cleaner] cpp/cmd/mrstats.cpp:17: + #include <vector> |
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| opt = get_options("output"); | ||
| fields.reserve(opt.size()); | ||
| for (size_t n = 0; n < opt.size(); ++n) | ||
| fields.push_back(MR::Enum::from_name<Stats::field_t>(opt[n][0])); | ||
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There was a problem hiding this comment. warning: 'push_back' is called inside a loop; consider pre-allocating the container capacity before the loop [performance-inefficient-vector-operation] cpp/cmd/mrstats.cpp:113: - for (size_t n = 0; n < opt.size(); ++n)
+ fields.reserve(opt.size());
+ for (size_t n = 0; n < opt.size(); ++n) |
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| if (App::log_level && fields.empty()) | ||
| Stats::print_header(is_complex); | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -21,11 +21,13 @@ | |
| #include "algo/copy.h" | ||
| #include "algo/loop.h" | ||
| #include "algo/threaded_copy.h" | ||
| #include "app.h" | ||
| #include "command.h" | ||
| #include "debug.h" | ||
| #include "dwi/directions/predefined.h" | ||
| #include "dwi/directions/validate.h" | ||
| #include "dwi/gradient.h" | ||
| #include "enum.h" | ||
| #include "file/matrix.h" | ||
| #include "file/nifti_utils.h" | ||
| #include "filter/reslice.h" | ||
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@@ -156,9 +158,9 @@ void usage() { | |
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| + Option ("interp", | ||
| std::string("set the interpolation method to use when reslicing") | ||
| + " (choices: " + MR::Enum::join<MR::Interp::interp_type>() + ";" | ||
| + " default: " + MR::Enum::lowercase_name(default_interp) + ").") | ||
| + Argument ("method").type_choice<MR::Interp::interp_type>() | ||
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| + Option ("oversample", | ||
| "set the amount of over-sampling (in the target space) to perform when regridding." | ||
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@@ -584,13 +586,9 @@ void run() { | |
| } | ||
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| // Interpolator | ||
| const MR::Interp::interp_type interp = get_option_choice<MR::Interp::interp_type>("interp", default_interp); | ||
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There was a problem hiding this comment. warning: no header providing "MR::App::get_option_choice" is directly included [misc-include-cleaner] const MR::Interp::interp_type interp = get_option_choice<MR::Interp::interp_type>("interp", default_interp);
^ |
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| if (!get_options("interp").empty() && !warp && !template_header) | ||
| WARN("interpolator choice ignored since the input image will not be regridded"); | ||
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| // over-sampling | ||
| std::vector<uint32_t> oversample = Adapter::AutoOverSample; | ||
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| Original file line number | Diff line number | Diff line change | ||||
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@@ -16,6 +16,7 @@ | |||||
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| #include <set> | ||||||
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| #include "app.h" | ||||||
| #include "command.h" | ||||||
| #include "image.h" | ||||||
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There was a problem hiding this comment. warning: included header enum.h is not used directly [misc-include-cleaner]
Suggested change
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| #include "thread_queue.h" | ||||||
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@@ -154,9 +155,7 @@ void execute(Image<node_t> &node_image, const node_t max_node_index, const std:: | |||||
| Metric metric; | ||||||
| Tractography::Connectome::setup_metric(metric, node_image); | ||||||
| std::unique_ptr<Tck2nodes_base> tck2nodes(load_assignment_mode(node_image)); | ||||||
| const stat_edge statistic = get_option_choice<stat_edge>("stat_edge", stat_edge::SUM); | ||||||
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There was a problem hiding this comment. warning: no header providing "MR::App::get_option_choice" is directly included [misc-include-cleaner] const stat_edge statistic = get_option_choice<stat_edge>("stat_edge", stat_edge::SUM);
^ |
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| // Prepare for reading the track data | ||||||
| Tractography::Properties properties; | ||||||
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@@ -191,7 +190,7 @@ void execute(Image<node_t> &node_image, const node_t max_node_index, const std:: | |||||
| get_options("symmetric").size(), | ||||||
| get_options("zero_diagonal").size()); | ||||||
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| auto opt = get_options("out_assignments"); | ||||||
| if (!opt.empty()) | ||||||
| connectome.write_assignments(opt[0][0]); | ||||||
| } | ||||||
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warning: no header providing "MR::App::get_option_choice" is directly included [misc-include-cleaner]