* lazzara/igr/gui/segmentation2dt/src/mln_data.cc, * lazzara/igr/gui/segmentation2dt/src/mln_data.hh: Add more temporary images. * lazzara/igr/gui/segmentation2dt/src/save_widget.cc: Add checkboxes to select which image to save. * lazzara/igr/gui/segmentation2dt/src/seg_widget.cc, * lazzara/igr/gui/segmentation2dt/src/seg_widget.hh, * lazzara/igr/gui/segmentation2dt/src/tools/seg.cc, * lazzara/igr/gui/segmentation2dt/src/tools/seg.hh, * lazzara/igr/gui/segmentation2dt/src/tools/mean_regions.cc: Compute non-filtered and linearly filtered image. * lazzara/igr/gui/segmentation2dt/src/task_widget.cc: Avoid a warning. * lazzara/igr/gui/segmentation2dt/src/tools/save.cc * lazzara/igr/gui/segmentation2dt/src/tools/save.hh: Allow to save more images. * lazzara/igr/gui/segmentation2dt/ui/plot_widget.ui, * lazzara/igr/gui/segmentation2dt/ui/save_widget.ui: Update widgets. * lazzara/igr/gui/shared/include/function_means.hh, * lazzara/igr/gui/shared/include/mean_function_per_region.hh, * lazzara/igr/gui/shared/include/normalization.hh: Add missing inlines. * lazzara/igr/gui/shared/include/mean_regions.hh, * lazzara/igr/gui/shared/include/time_smooth_morpho.hh: Add missing includes. --- milena/sandbox/ChangeLog | 37 +++++++ .../igr/gui/segmentation2dt/src/mln_data.cc | 112 +++++++++++++++----- .../igr/gui/segmentation2dt/src/mln_data.hh | 50 ++++++--- .../igr/gui/segmentation2dt/src/save_widget.cc | 21 ++++ .../igr/gui/segmentation2dt/src/seg_widget.cc | 30 ++++-- .../igr/gui/segmentation2dt/src/seg_widget.hh | 3 +- .../igr/gui/segmentation2dt/src/task_widget.cc | 2 +- .../gui/segmentation2dt/src/tools/mean_regions.cc | 72 +++++++++++-- .../igr/gui/segmentation2dt/src/tools/save.cc | 90 +++++++++++++--- .../igr/gui/segmentation2dt/src/tools/save.hh | 12 ++- .../igr/gui/segmentation2dt/src/tools/seg.cc | 60 +++++++++-- .../igr/gui/segmentation2dt/src/tools/seg.hh | 10 ++- .../igr/gui/segmentation2dt/ui/plot_widget.ui | 20 ++++ .../igr/gui/segmentation2dt/ui/save_widget.ui | 80 +++++++++++++-- .../igr/gui/shared/include/function_means.hh | 1 - .../gui/shared/include/mean_function_per_region.hh | 2 +- .../lazzara/igr/gui/shared/include/mean_regions.hh | 2 + .../igr/gui/shared/include/normalization.hh | 1 - .../igr/gui/shared/include/time_smooth_morpho.hh | 2 + 19 files changed, 508 insertions(+), 99 deletions(-) diff --git a/milena/sandbox/ChangeLog b/milena/sandbox/ChangeLog index 677070c..4f62abc 100644 --- a/milena/sandbox/ChangeLog +++ b/milena/sandbox/ChangeLog @@ -1,5 +1,42 @@ 2010-11-15 Guillaume Lazzara &lt;z(a)lrde.epita.fr&gt; + Allow to save results filtered differently in the 3D segmentation + tool. + + * lazzara/igr/gui/segmentation2dt/src/mln_data.cc, + * lazzara/igr/gui/segmentation2dt/src/mln_data.hh: Add more + temporary images. + + * lazzara/igr/gui/segmentation2dt/src/save_widget.cc: Add + checkboxes to select which image to save. + + * lazzara/igr/gui/segmentation2dt/src/seg_widget.cc, + * lazzara/igr/gui/segmentation2dt/src/seg_widget.hh, + * lazzara/igr/gui/segmentation2dt/src/tools/seg.cc, + * lazzara/igr/gui/segmentation2dt/src/tools/seg.hh, + * lazzara/igr/gui/segmentation2dt/src/tools/mean_regions.cc: + Compute non-filtered and linearly filtered image. + + * lazzara/igr/gui/segmentation2dt/src/task_widget.cc: Avoid a warning. + + * lazzara/igr/gui/segmentation2dt/src/tools/save.cc + * lazzara/igr/gui/segmentation2dt/src/tools/save.hh: Allow to save + more images. + + * lazzara/igr/gui/segmentation2dt/ui/plot_widget.ui, + * lazzara/igr/gui/segmentation2dt/ui/save_widget.ui: Update widgets. + + * lazzara/igr/gui/shared/include/function_means.hh, + * lazzara/igr/gui/shared/include/mean_function_per_region.hh, + * lazzara/igr/gui/shared/include/normalization.hh: Add missing + inlines. + + * lazzara/igr/gui/shared/include/mean_regions.hh, + * lazzara/igr/gui/shared/include/time_smooth_morpho.hh: Add + missing includes. + +2010-11-15 Guillaume Lazzara &lt;z(a)lrde.epita.fr&gt; + * lazzara/igr/gui/segmentation/src/main_window.cc: Avoid a warning in 2D segmentation tool. diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/mln_data.cc b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/mln_data.cc index c294c73..f8dc7c8 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/mln_data.cc +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/mln_data.cc @@ -295,19 +295,19 @@ namespace igr } - void mln_data::update_seg(const image3d<seg_data_t>& seg, - const seg_data_t& nregion) + void mln_data::update_seg_smooth(const image3d<seg_data_t>& seg, + const seg_data_t& nregion) { - update_seg(seg, nregion, 0); + update_seg_smooth(seg, nregion, 0); } - void mln_data::update_seg(const image3d<seg_data_t>& seg, - const seg_data_t& nregion, - int sli) + void mln_data::update_seg_smooth(const image3d<seg_data_t>& seg, + const seg_data_t& nregion, + int sli) { - seg_ = seg; - initialize(seg_dsp_, seg_); + seg_smooth_ = seg; + initialize(seg_dsp_, seg_smooth_); // This random function was found here: // http://en.wikipedia.org/wiki/Random_number_generation @@ -324,8 +324,8 @@ namespace igr for_all(p) { value::hsl_<float,float,float> hsl__( - h_values[seg_(p)], -// (unsigned(seg_(p)) * 10) % 359 + 1, + h_values[seg_smooth_(p)], +// (unsigned(seg_smooth_(p)) * 10) % 359 + 1, 1, unsigned(in_(p)) * .002745f); // = 1 / 255 * 0.7); convert::from_to(hsl__, seg_dsp_(p)); @@ -334,22 +334,51 @@ namespace igr // Make sure there is no border! extension::adjust(seg_dsp_, 0); - nregion_ = nregion; + nregion_smooth_ = nregion; emit image_layer_count(seg_dsp_.nslis()); compute_new_seg_image(sli); } - void mln_data::update_mean_regions(const image3d<input_data_t>& mean_regions) + + void mln_data::update_seg(const image3d<seg_data_t>& seg, + const seg_data_t& nregion) { - update_mean_regions(mean_regions, 0); + seg_ = seg; + nregion_ = nregion; } - void mln_data::update_mean_regions(const image3d<input_data_t>& mean_regions, - int sli) + void mln_data::update_seg_smooth_linear(const image3d<seg_data_t>& seg, + const seg_data_t& nregion) + { + seg_smooth_linear_ = seg; + nregion_smooth_linear_ = nregion; + } + + + void mln_data::update_mean_regions(const image3d<input_data_t>& mean_regions) { mean_regions_ = mean_regions; + } + + + void mln_data::update_mean_regions_smooth_linear(const image3d<input_data_t>& mean_regions) + { + mean_regions_smooth_linear_ = mean_regions; + } + + + void mln_data::update_mean_regions_smooth(const image3d<input_data_t>& mean_regions) + { + update_mean_regions_smooth(mean_regions, 0); + } + + + void mln_data::update_mean_regions_smooth(const image3d<input_data_t>& mean_regions, + int sli) + { + mean_regions_smooth_ = mean_regions; mean_regions_dsp_ = data::convert(dsp_data_t(), data::stretch(value::int_u8(), mean_regions)); @@ -368,7 +397,7 @@ namespace igr } - const mln_data::in_t& + const in_t& mln_data::in() const { return in_; @@ -380,38 +409,50 @@ namespace igr } - const mln_data::ref_mean_t& + const ref_mean_t& mln_data::ref_mean() const { return ref_mean_; } - const mln_data::norm_smooth_t& + const norm_smooth_t& mln_data::norm() const { return norm_; } - const mln_data::norm_smooth_t& + const norm_smooth_t& mln_data::norm_smooth() const { return norm_smooth_; } - const mln_data::norm_smooth_t& + const norm_smooth_t& mln_data::norm_smooth_linear() const { return norm_smooth_linear_; } - const mln_data::seg_t& + const seg_t& mln_data::seg() const { return seg_; } + const seg_t& + mln_data::seg_smooth_linear() const + { + return seg_smooth_linear_; + } + + const seg_t& + mln_data::seg_smooth() const + { + return seg_smooth_; + } + unsigned mln_data::seg_nslis() const { return seg_.nslis(); @@ -422,24 +463,45 @@ namespace igr return nregion_; } + const seg_data_t& mln_data::nregion_smooth_linear() const + { + return nregion_smooth_linear_; + } + + const seg_data_t& mln_data::nregion_smooth() const + { + return nregion_smooth_; + } - const mln_data::seg_dsp_t& mln_data::seg_dsp() const + const seg_dsp_t& mln_data::seg_dsp() const { return seg_dsp_; } - mln_data::seg_dsp_t& mln_data::seg_dsp() + seg_dsp_t& mln_data::seg_dsp() { return seg_dsp_; } - const mln_data::mean_regions_t& + const mean_regions_t& mln_data::mean_regions() const { return mean_regions_; } - const mln_data::mean_regions_dsp_t& + const mean_regions_t& + mln_data::mean_regions_smooth_linear() const + { + return mean_regions_smooth_linear_; + } + + const mean_regions_t& + mln_data::mean_regions_smooth() const + { + return mean_regions_smooth_; + } + + const mean_regions_dsp_t& mln_data::mean_regions_dsp() const { return mean_regions_dsp_; diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/mln_data.hh b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/mln_data.hh index 6f1776f..bc75ecb 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/mln_data.hh +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/mln_data.hh @@ -26,22 +26,23 @@ namespace igr }; + typedef image3d<igr::input_data_t> in_t; + typedef image3d<igr::dsp_data_t> in_dsp_t; + typedef image2d<igr::mean_t> ref_mean_t; + typedef image2d<igr::dsp_data_t> ref_mean_dsp_t; + typedef image3d<igr::smoothed_data_t> norm_smooth_t; + typedef image3d<igr::dsp_data_t> norm_smooth_dsp_t; + typedef image3d<igr::seg_data_t> seg_t; + typedef image3d<igr::dsp_data_t> seg_dsp_t; + typedef image3d<igr::input_data_t> mean_regions_t; + typedef image3d<igr::dsp_data_t> mean_regions_dsp_t; + + class mln_data : public QObject { Q_OBJECT; public: - typedef image3d<igr::input_data_t> in_t; - typedef image3d<igr::dsp_data_t> in_dsp_t; - typedef image2d<igr::mean_t> ref_mean_t; - typedef image2d<igr::dsp_data_t> ref_mean_dsp_t; - typedef image3d<igr::smoothed_data_t> norm_smooth_t; - typedef image3d<igr::dsp_data_t> norm_smooth_dsp_t; - typedef image3d<igr::seg_data_t> seg_t; - typedef image3d<igr::dsp_data_t> seg_dsp_t; - typedef image3d<igr::input_data_t> mean_regions_t; - typedef image3d<igr::dsp_data_t> mean_regions_dsp_t; - mln_data(); ~mln_data(); @@ -83,12 +84,19 @@ namespace igr void update_norm_smooth(const image3d<smoothed_data_t>& norm_smooth); void update_norm_smooth_linear(const image3d<smoothed_data_t>& norm_smooth_linear); + void update_seg_smooth(const image3d<seg_data_t>& seg, + const seg_data_t& nregion); + void update_seg_smooth(const image3d<seg_data_t>& seg, + const seg_data_t& nregion, int sli); void update_seg(const image3d<seg_data_t>& seg, - const seg_data_t& nregion); - void update_seg(const image3d<seg_data_t>& seg, - const seg_data_t& nregion, int sli); + const seg_data_t& nregion); + void update_seg_smooth_linear(const image3d<seg_data_t>& seg, + const seg_data_t& nregion); + void update_mean_regions(const image3d<input_data_t>& mean_regions); - void update_mean_regions(const image3d<input_data_t>& mean_regions, int sli); + void update_mean_regions_smooth_linear(const image3d<input_data_t>& mean_regions); + void update_mean_regions_smooth(const image3d<input_data_t>& mean_regions); + void update_mean_regions_smooth(const image3d<input_data_t>& mean_regions, int sli); const std::string& filename() const; @@ -104,13 +112,19 @@ namespace igr const norm_smooth_t& norm_smooth_linear() const; const seg_t& seg() const; + const seg_t& seg_smooth_linear() const; + const seg_t& seg_smooth() const; unsigned seg_nslis() const; const seg_data_t& nregion() const; + const seg_data_t& nregion_smooth_linear() const; + const seg_data_t& nregion_smooth() const; const seg_dsp_t& seg_dsp() const; seg_dsp_t& seg_dsp(); const mean_regions_t& mean_regions() const; + const mean_regions_t& mean_regions_smooth_linear() const; + const mean_regions_t& mean_regions_smooth() const; const mean_regions_dsp_t& mean_regions_dsp() const; const log_data& logs() const; @@ -173,10 +187,16 @@ namespace igr norm_smooth_t norm_smooth_linear_; seg_t seg_; + seg_t seg_smooth_linear_; + seg_t seg_smooth_; seg_dsp_t seg_dsp_; igr::seg_data_t nregion_; + igr::seg_data_t nregion_smooth_linear_; + igr::seg_data_t nregion_smooth_; mean_regions_t mean_regions_; + mean_regions_t mean_regions_smooth_linear_; + mean_regions_t mean_regions_smooth_; mean_regions_dsp_t mean_regions_dsp_; log_data logs_; diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/save_widget.cc b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/save_widget.cc index 8d87133..576c6ba 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/save_widget.cc +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/save_widget.cc @@ -113,13 +113,34 @@ namespace igr if (logCBox->isChecked()) selected.append(tools::Log); + if (meanFunCBox->isChecked()) + { selected.append(tools::MeanFunctions); + + if (meanFunNonFilteredCBox->isChecked()) + selected.append(tools::MeanFunctionsNonFiltered); + if (meanFunLinearFilterCBox->isChecked()) + selected.append(tools::MeanFunctionsLinearFilter); + if (meanFunMorphoFilterCBox->isChecked()) + selected.append(tools::MeanFunctionsMorphoFilter); + } + if (refImaCBox->isChecked()) selected.append(tools::RefImage); + if (segImaCBox->isChecked()) + { selected.append(tools::SegImage); + if (segImaNonFilteredCBox->isChecked()) + selected.append(tools::SegImageNonFiltered); + if (segImaLinearFilterCBox->isChecked()) + selected.append(tools::SegImageLinearFilter); + if (segImaMorphoFilterCBox->isChecked()) + selected.append(tools::SegImageMorphoFilter); + } + return selected; } diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/seg_widget.cc b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/seg_widget.cc index 6891432..ff49690 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/seg_widget.cc +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/seg_widget.cc @@ -43,7 +43,8 @@ namespace igr { seg_widget::seg_widget(QWidget *parent) - : Task_Widget(parent) + : Task_Widget(parent), + compute_preview_(false), preview_computed_(false) { setupUi(this); } @@ -63,6 +64,7 @@ namespace igr connect(viewer_, SIGNAL(slider_valueChanged(int)), data_, SLOT(compute_new_seg_image(int))); + compute_preview_ = true; emit task_ready(); } @@ -73,6 +75,7 @@ namespace igr set_data_and_connections(); clearBtn->setEnabled(false); nregion_lbl->setText(""); + preview_computed_ = false; viewer_->set_image_layer_count(data_->in_nslis()); } @@ -105,7 +108,7 @@ namespace igr void seg_widget::run_task_(task_handler& handler) { tools::seg* - task = new tools::seg(data_, get_lambda_value()); + task = new tools::seg(data_, get_lambda_value(), compute_preview_, preview_computed_); connect(&handler, SIGNAL(finished()), this, SLOT(task_finished_slot())); @@ -118,8 +121,8 @@ namespace igr { point3d p3d(viewer_->current_slice(), p.y(), p.x()); - if (clearBtn->isEnabled()) // A segmentation have been computed - return data_->seg().domain().has(p3d); + if (preview_computed_) // A segmentation have been computed + return data_->seg_smooth().domain().has(p3d); else return data_->norm_smooth().domain().has(p3d); } @@ -128,8 +131,8 @@ namespace igr float seg_widget::compute_mouseover_data(const QPointF& p) const { point3d p3d(viewer_->current_slice(), p.y(), p.x()); - if (clearBtn->isEnabled()) // A segmentation have been computed - return float(data_->seg()(p3d)); + if (preview_computed_) // A segmentation have been computed + return float(data_->seg_smooth()(p3d)); else return float(data_->norm_smooth()(p3d)); } @@ -163,8 +166,14 @@ namespace igr this, SLOT(task_finished_slot())); clearBtn->setEnabled(true); - this->already_computed_ = true; - nregion_lbl->setText(tr("%1 regions").arg(data_->nregion())); + if (!compute_preview_) + this->already_computed_ = true; + else + { + compute_preview_ = false; + preview_computed_ = true; + } + nregion_lbl->setText(tr("%1 regions").arg(data_->nregion_smooth())); // Result already refreshed and displayed. } @@ -172,26 +181,31 @@ namespace igr void seg_widget::on_filter_1_clicked(bool) { this->already_computed_ = false; + preview_computed_ = false; } void seg_widget::on_filter_2_clicked(bool) { this->already_computed_ = false; + preview_computed_ = false; } void seg_widget::on_filter_3_clicked(bool) { this->already_computed_ = false; + preview_computed_ = false; } void seg_widget::on_filter_4_clicked(bool) { this->already_computed_ = false; + preview_computed_ = false; } void seg_widget::on_filter_5_clicked(bool) { this->already_computed_ = false; + preview_computed_ = false; } } // end of namespace igr::segmentation diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/seg_widget.hh b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/seg_widget.hh index bed5e24..26e35fe 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/seg_widget.hh +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/seg_widget.hh @@ -68,7 +68,8 @@ namespace igr unsigned get_lambda_value() const; private: // Attributes - + bool compute_preview_; + bool preview_computed_; }; diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/task_widget.cc b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/task_widget.cc index e3ddce5..c8e6cbc 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/task_widget.cc +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/task_widget.cc @@ -55,7 +55,7 @@ namespace igr handler.no_op(); } - void Task_Widget::run_task_(task_handler& handler) + void Task_Widget::run_task_(task_handler& /*handler*/) { qDebug() << "WARNING: task_widget::run_task_ should not be called..."; } diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/mean_regions.cc b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/mean_regions.cc index 8245a70..6ae3b47 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/mean_regions.cc +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/mean_regions.cc @@ -32,23 +32,75 @@ namespace igr void mean_regions::run() { - seg_data_t nregion = data_->nregion(); - image3d<seg_data_t> - seg_packed = labeling::pack(data_->seg(), nregion); + // No filter + { + // FIXME: computed twice? here and in save.cc ? + seg_data_t nregion = data_->nregion(); + image3d<seg_data_t> + seg_packed = labeling::pack(data_->seg(), nregion); - emit next_step(); + emit next_step(); + + data_->update_seg(seg_packed, nregion); + + emit next_step(); + + image3d<input_data_t> + means = shared::mean_regions(data_->in(), + data_->seg(), data_->nregion()); + + emit next_step(); - data_->update_seg(seg_packed, nregion); + data_->update_mean_regions(means); + } emit next_step(); - image3d<input_data_t> - means = shared::mean_regions(data_->in(), - data_->seg(), data_->nregion()); + // Linear filter + { + // FIXME: computed twice? here and in save.cc ? + seg_data_t nregion = data_->nregion_smooth_linear(); + image3d<seg_data_t> + seg_packed = labeling::pack(data_->seg_smooth_linear(), nregion); + + emit next_step(); + + data_->update_seg_smooth_linear(seg_packed, nregion); + + emit next_step(); + + image3d<input_data_t> + means = shared::mean_regions(data_->in(), + data_->seg_smooth_linear(), data_->nregion_smooth_linear()); + + emit next_step(); + + data_->update_mean_regions_smooth_linear(means); + } emit next_step(); - data_->update_mean_regions(means); + // Morpho filter + { + // FIXME: computed twice? here and in save.cc ? + seg_data_t nregion = data_->nregion_smooth(); + image3d<seg_data_t> + seg_packed = labeling::pack(data_->seg_smooth(), nregion); + + emit next_step(); + + data_->update_seg_smooth(seg_packed, nregion); + + emit next_step(); + + image3d<input_data_t> + means = shared::mean_regions(data_->in(), + data_->seg_smooth(), data_->nregion_smooth()); + + emit next_step(); + + data_->update_mean_regions_smooth(means); + } } @@ -60,7 +112,7 @@ namespace igr unsigned mean_regions::step_count() const { - return 4; + return 12; } diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/save.cc b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/save.cc index 23e38d1..185ed86 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/save.cc +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/save.cc @@ -104,6 +104,20 @@ namespace igr return true; } + void save::save_mean_funs(const seg_t& pseg, const seg_data_t& pnlabels, + const mean_regions_t& mean_regions, const QString& prefix) + { + QString output_base = basedir_ + "/" + prefix; + util::array<util::array<input_data_t> > + functions = shared::mean_function_per_region(mean_regions, pseg, pnlabels); + + for (unsigned i = 1; i < functions.nelements(); ++i) + { + QString name = output_base + "_l" + QString::number(i) + ".plot"; + mln::io::plot::save(functions[i], name.toStdString()); + } + } + void save::run() { @@ -111,12 +125,19 @@ namespace igr QString basename = f.baseName(); QString output; - - seg_data_t packed_nlabels; - image3d<seg_data_t> packed_seg; - if (selected_.contains(SegImage) || selected_.contains(MeanFunctions)) - packed_seg = labeling::pack(data_->seg(), packed_nlabels); +// seg_data_t pnlabels, pnlabels_smooth, pnlabels_smooth_linear; +// image3d<seg_data_t> +// pseg, pseg_smooth, pseg_smooth_linear; + + // Preparing some common data. +// if (selected_.contains(SegImageNonFiltered) || selected_.contains(MeanFunctionsNonFiltered)) +// pseg = labeling::pack(data_->seg(), pnlabels); +// if (selected_.contains(SegImageLinearFilter) || selected_.contains(MeanFunctionsLinearFilter)) +// pseg_smooth_linear = labeling::pack(data_->seg_smooth_linear(), pnlabels_smooth_linear); +// if (selected_.contains(SegImageMorphoFilter) || selected_.contains(MeanFunctionsMorphoFilter)) +// pseg_smooth = labeling::pack(data_->seg_smooth(), pnlabels_smooth); + foreach(SavedData e, selected_) { @@ -135,24 +156,57 @@ namespace igr emit next_step(); break; - case SegImage: - output = basedir_ + "/" + basename + "_segmentation.raw"; - io::raw::save(packed_seg, output.toStdString()); + + // Segmentations + + case SegImageNonFiltered: + output = basedir_ + "/" + basename + "_segmentation_non_filtered.raw"; + io::raw::save(data_->seg(), output.toStdString()); + emit next_step(); + break; + + case SegImageLinearFilter: + output = basedir_ + "/" + basename + "_segmentation_linear_filter.raw"; + io::raw::save(data_->seg_smooth_linear(), output.toStdString()); emit next_step(); break; + case SegImageMorphoFilter: + output = basedir_ + "/" + basename + "_segmentation_morpho_filter.raw"; + io::raw::save(data_->seg_smooth(), output.toStdString()); + emit next_step(); + break; + + + // Mean functions + + case MeanFunctionsNonFiltered: + save_mean_funs(data_->seg(), data_->nregion(), data_->mean_regions(), + basename + "_non_filtered"); + emit next_step(); + break; + + case MeanFunctionsLinearFilter: + save_mean_funs(data_->seg_smooth_linear(), data_->nregion_smooth_linear(), + data_->mean_regions_smooth_linear(), + basename + "_linear_filter"); + emit next_step(); + break; + + case MeanFunctionsMorphoFilter: + save_mean_funs(data_->seg_smooth(), data_->nregion_smooth(), + data_->mean_regions_smooth(), + basename + "_morpho_filter"); + emit next_step(); + break; + + + default: + case SegImage: case MeanFunctions: - QString output_base = basedir_ + "/" + basename; - util::array<util::array<input_data_t> > - functions = shared::mean_function_per_region(data_->mean_regions(), - packed_seg, packed_nlabels); - - for (unsigned i = 1; i < functions.nelements(); ++i) - { - QString name = output_base + "_l" + QString::number(i) + ".plot"; - io::plot::save(functions[i], name.toStdString()); - } + // Nothing. emit next_step(); + break; } } diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/save.hh b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/save.hh index fc30282..53b61fe 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/save.hh +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/save.hh @@ -26,7 +26,13 @@ namespace igr Log, RefImage, SegImage, - MeanFunctions + SegImageNonFiltered, + SegImageLinearFilter, + SegImageMorphoFilter, + MeanFunctions, + MeanFunctionsNonFiltered, + MeanFunctionsLinearFilter, + MeanFunctionsMorphoFilter }; @@ -59,6 +65,10 @@ namespace igr private: // Members bool save_log(const QString& output); + void save_mean_funs(const seg_t& pseg, + const seg_data_t& pnlabels, + const mean_regions_t& mean_regions, + const QString& prefix); private: // attributes mln_data* data_; diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/seg.cc b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/seg.cc index b57a52f..3769dc4 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/seg.cc +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/seg.cc @@ -34,9 +34,20 @@ namespace igr - seg::seg(mln_data* data, unsigned lambda) - : data_(data), lambda_(lambda) + seg::seg(mln_data* data, unsigned lambda, + bool compute_preview, bool preview_computed) + : data_(data), lambda_(lambda), + compute_preview_(compute_preview), + preview_computed_(preview_computed) { + // Setting step_count according to options. + if (compute_preview) + step_count_ = 3; + else + if (preview_computed) + step_count_ = 6; + else + step_count_ = 9; } @@ -45,12 +56,11 @@ namespace igr } - void seg::run() + const image3d<seg_data_t> seg::compute_seg(const image3d<igr::smoothed_data_t>& norm, + seg_data_t& nregion) { - seg_data_t nregion; image2d<seg_data_t> - tmp = shared::time_segmentation(data_->norm_smooth(), - nregion, lambda_); + tmp = shared::time_segmentation(norm, nregion, lambda_); emit next_step(); @@ -58,7 +68,41 @@ namespace igr emit next_step(); - data_->update_seg(wsd, nregion); + return wsd; + } + + + void seg::run() + { + // Compute result on morpho smooth image only. + if (compute_preview_ || !preview_computed_) + { + seg_data_t nregion; + image3d<seg_data_t> wsd = compute_seg(data_->norm_smooth(), nregion); + data_->update_seg_smooth(wsd, nregion); + } + + if (!compute_preview_) + { + if (!preview_computed_) + emit next_step(); + + // Non filtered image. + { + seg_data_t nregion; + image3d<seg_data_t> wsd = compute_seg(data_->norm(), nregion); + data_->update_seg(wsd, nregion); + } + + emit next_step(); + + // Linearly filtered image. + { + seg_data_t nregion; + image3d<seg_data_t> wsd = compute_seg(data_->norm_smooth_linear(), nregion); + data_->update_seg_smooth_linear(wsd, nregion); + } + } } @@ -70,7 +114,7 @@ namespace igr unsigned seg::step_count() const { - return 3; + return step_count_; } diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/seg.hh b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/seg.hh index 0e3d75e..f2efc90 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/seg.hh +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/src/tools/seg.hh @@ -26,7 +26,8 @@ namespace igr Q_OBJECT; public: - seg(mln_data* data, unsigned lambda); + seg(mln_data* data, unsigned lambda, + bool compute_preview, bool preview_computed); ~seg(); void run(); @@ -46,9 +47,16 @@ namespace igr /// @} + private: // methods + const image3d<seg_data_t> compute_seg(const image3d<igr::smoothed_data_t>& norm, + seg_data_t& nregion); + private: // attributes mln_data* data_; unsigned lambda_; + bool compute_preview_; + bool preview_computed_; + unsigned step_count_; }; } // end of namespace igr::segmentation::tools diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/ui/plot_widget.ui b/milena/sandbox/lazzara/igr/gui/segmentation2dt/ui/plot_widget.ui index adbc296..18d8e91 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/ui/plot_widget.ui +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/ui/plot_widget.ui @@ -71,6 +71,26 @@ </widget> </item> <item> + <widget class="Line" name="line" > + <property name="orientation" > + <enum>Qt::Vertical</enum> + </property> + </widget> + </item> + <item> + <widget class="QPushButton" name="savePlotBtn_" > + <property name="maximumSize" > + <size> + <width>16777215</width> + <height>20</height> + </size> + </property> + <property name="text" > + <string>Save plot</string> + </property> + </widget> + </item> + <item> <spacer name="horizontalSpacer_2" > <property name="orientation" > <enum>Qt::Horizontal</enum> diff --git a/milena/sandbox/lazzara/igr/gui/segmentation2dt/ui/save_widget.ui b/milena/sandbox/lazzara/igr/gui/segmentation2dt/ui/save_widget.ui index c832560..641cea6 100644 --- a/milena/sandbox/lazzara/igr/gui/segmentation2dt/ui/save_widget.ui +++ b/milena/sandbox/lazzara/igr/gui/segmentation2dt/ui/save_widget.ui @@ -6,7 +6,7 @@ <x>0</x> <y>0</y> <width>370</width> - <height>362</height> + <height>470</height> </rect> </property> <property name="sizePolicy" > @@ -161,23 +161,87 @@ p, li { white-space: pre-wrap; } </widget> </item> <item> - <widget class="QCheckBox" name="segImaCBox" > - <property name="text" > + <widget class="QGroupBox" name="segImaCBox" > + <property name="title" > <string>Segmentation image</string> </property> - <property name="checked" > + <property name="checkable" > <bool>true</bool> </property> + <layout class="QVBoxLayout" name="verticalLayout_5" > + <item> + <widget class="QCheckBox" name="segImaNonFilteredCBox" > + <property name="text" > + <string>Non-filtered</string> + </property> + <property name="checked" > + <bool>true</bool> + </property> + </widget> + </item> + <item> + <widget class="QCheckBox" name="segImaLinearFilterCBox" > + <property name="text" > + <string>Linear filter</string> + </property> + <property name="checked" > + <bool>true</bool> + </property> + </widget> + </item> + <item> + <widget class="QCheckBox" name="segImaMorphoFilterCBox" > + <property name="text" > + <string>Morphological filter</string> + </property> + <property name="checked" > + <bool>true</bool> + </property> + </widget> + </item> + </layout> </widget> </item> <item> - <widget class="QCheckBox" name="meanFunCBox" > - <property name="text" > - <string>Mean function per region </string> + <widget class="QGroupBox" name="meanFunCBox" > + <property name="title" > + <string>Mean function per region</string> </property> - <property name="checked" > + <property name="checkable" > <bool>true</bool> </property> + <layout class="QVBoxLayout" name="verticalLayout_4" > + <item> + <widget class="QCheckBox" name="meanFunNonFilteredCBox" > + <property name="text" > + <string>Non-filtered</string> + </property> + <property name="checked" > + <bool>true</bool> + </property> + </widget> + </item> + <item> + <widget class="QCheckBox" name="meanFunLinearFilterCBox" > + <property name="text" > + <string>Linear filter</string> + </property> + <property name="checked" > + <bool>true</bool> + </property> + </widget> + </item> + <item> + <widget class="QCheckBox" name="meanFunMorphoFilterCBox" > + <property name="text" > + <string>Morphological filter</string> + </property> + <property name="checked" > + <bool>true</bool> + </property> + </widget> + </item> + </layout> </widget> </item> </layout> diff --git a/milena/sandbox/lazzara/igr/gui/shared/include/function_means.hh b/milena/sandbox/lazzara/igr/gui/shared/include/function_means.hh index bdc2098..18cb65a 100644 --- a/milena/sandbox/lazzara/igr/gui/shared/include/function_means.hh +++ b/milena/sandbox/lazzara/igr/gui/shared/include/function_means.hh @@ -49,7 +49,6 @@ namespace igr /// Compute from slice \p sli_first to \p sli_last included. // template <typename V> - inline image2d<float> function_means(const image3d<V>& ima, int sli_first, int sli_last); diff --git a/milena/sandbox/lazzara/igr/gui/shared/include/mean_function_per_region.hh b/milena/sandbox/lazzara/igr/gui/shared/include/mean_function_per_region.hh index b0adcfc..75da3a8 100644 --- a/milena/sandbox/lazzara/igr/gui/shared/include/mean_function_per_region.hh +++ b/milena/sandbox/lazzara/igr/gui/shared/include/mean_function_per_region.hh @@ -30,6 +30,7 @@ #ifndef IGR_SHARED_INCLUDE_MEAN_FUNCTION_PER_REGION_HH # define IGR_SHARED_INCLUDE_MEAN_FUNCTION_PER_REGION_HH +# include <mln/core/var.hh> # include <mln/core/image/image3d.hh> # include <mln/core/image/dmorph/slice_image.hh> @@ -49,7 +50,6 @@ namespace igr /// Compute from slice \p sli_first to \p sli_last included. // template <typename V, typename L> - inline util::array<util::array<V> > mean_function_per_region(const image3d<V>& ima, const image3d<L>& lbl, const L& nregion); diff --git a/milena/sandbox/lazzara/igr/gui/shared/include/mean_regions.hh b/milena/sandbox/lazzara/igr/gui/shared/include/mean_regions.hh index 85a2e7d..6872683 100644 --- a/milena/sandbox/lazzara/igr/gui/shared/include/mean_regions.hh +++ b/milena/sandbox/lazzara/igr/gui/shared/include/mean_regions.hh @@ -34,6 +34,8 @@ # include <mln/core/image/image2d.hh> # include <mln/core/image/dmorph/slice_image.hh> +# include <mln/core/var.hh> + # include <mln/data/paste.hh> # include <mln/labeling/mean_values.hh> # include <mln/labeling/pack.hh> diff --git a/milena/sandbox/lazzara/igr/gui/shared/include/normalization.hh b/milena/sandbox/lazzara/igr/gui/shared/include/normalization.hh index 6ec41a2..e4d91eb 100644 --- a/milena/sandbox/lazzara/igr/gui/shared/include/normalization.hh +++ b/milena/sandbox/lazzara/igr/gui/shared/include/normalization.hh @@ -56,7 +56,6 @@ namespace igr /// number of slices of \p input. // template <typename V1, typename V2> - inline image3d<float> normalization(const image3d<V1>& ima, const image2d<V2>& mean); diff --git a/milena/sandbox/lazzara/igr/gui/shared/include/time_smooth_morpho.hh b/milena/sandbox/lazzara/igr/gui/shared/include/time_smooth_morpho.hh index 4515e16..27331a0 100644 --- a/milena/sandbox/lazzara/igr/gui/shared/include/time_smooth_morpho.hh +++ b/milena/sandbox/lazzara/igr/gui/shared/include/time_smooth_morpho.hh @@ -31,6 +31,8 @@ # define IGR_SHARED_INCLUDE_TIME_SMOOTH_MORPHO_HH # include <mln/core/image/image3d.hh> +# include <mln/accu/stat/mean.hh> +# include <mln/accu/image/all.hh> # include <mln/morpho/closing/structural.hh> # include <mln/morpho/opening/structural.hh> # include <mln/win/sline3d.hh> -- 1.5.6.5