Mercurial > repos > rv43 > tomo
changeset 43:0b9ce9489ecc draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
| author | rv43 |
|---|---|
| date | Thu, 21 Apr 2022 16:12:21 +0000 |
| parents | 009d2d45ac79 |
| children | 0ac719053d6f |
| files | tomo.py |
| diffstat | 1 files changed, 17 insertions(+), 5 deletions(-) [+] |
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--- a/tomo.py Thu Apr 21 15:11:16 2022 +0000 +++ b/tomo.py Thu Apr 21 16:12:21 2022 +0000 @@ -836,6 +836,7 @@ tmp_max = tmp.max() tmp[img_x_bounds[0],:] = tmp_max tmp[img_x_bounds[1]-1,:] = tmp_max + title = f'tomography image at theta={self.config["theta_range"]["start"]}' msnc.quickImshow(tmp, title=title) del tmp x_sum_min = x_sum.min() @@ -870,7 +871,7 @@ tmp_max = tmp.max() tmp[img_x_bounds[0],:] = tmp_max tmp[img_x_bounds[1]-1,:] = tmp_max - title = 'Bright field' + title = 'bright field' msnc.quickImshow(tmp, title=title) del tmp msnc.quickPlot((range(x_sum.size), x_sum), @@ -904,7 +905,7 @@ tmp_max = tmp.max() tmp[x_low,:] = tmp_max tmp[x_upp-1,:] = tmp_max - title = 'Bright field' + title = 'bright field' msnc.quickImshow(tmp, title=title) del tmp msnc.quickPlot((range(x_sum.size), x_sum), @@ -940,9 +941,14 @@ tomo_stack[img_x_bounds[0],:] = tomo_stack_max tomo_stack[img_x_bounds[1]-1,:] = tomo_stack_max title = f'tomography image at theta={self.config["theta_range"]["start"]}' - msnc.quickImshow(tomo_stack, title=title, path='setup_pngs', - name=f'tomo_{stack["index"]}.png', save_fig=self.save_plots, save_only=True, - show_grid=True) + if self.galaxy_flag: + msnc.quickImshow(tomo_stack, title=title, path='setup_pngs', + name=f'tomo_{stack["index"]}.png', save_fig=True, save_only=True, + show_grid=True) + else: + msnc.quickImshow(tomo_stack, title=title, path=self.output_folder, + name=f'tomo_{stack["index"]}.png', save_fig=self.save_plots, + save_only=True, show_grid=True) del tomo_stack logging.debug(f'img_x_bounds: {img_x_bounds}') @@ -1848,8 +1854,10 @@ use_row = 'no' use_center = 'no' row = center_rows[0] + print('Ok1') if self.test_mode or self.galaxy_flag: assert(msnc.is_int(row, n1, n2-2)) + print('Ok2') if msnc.is_int(row, n1, n2-2): if self.test_mode or self.galaxy_flag: use_row = 'yes' @@ -1864,6 +1872,7 @@ if msnc.is_num(center_offset): use_center = pyip.inputYesNo('Current lower center offset = '+ f'{center_offset}, use this value ([y]/n)? ', blank=True) + print(f'Ok3 {use_center} {use_row}') if use_center == 'no': if use_row == 'no': if not self.test_mode: @@ -1876,10 +1885,13 @@ if self.save_plots_only: msnc.clearFig(f'theta={theta_start}') # center_stack order: row,theta,column + print('Ok4') center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg, eff_pixel_size, cross_sectional_dim, num_core=num_core, galaxy_param=galaxy_param) + print('Ok5') logging.info(f'lower_center_offset = {center_offset:.2f} {type(center_offset)}') + print('Ok6') # Update config and save to file find_center['row_bounds'] = [n1, n2]