Brain forms

This module defines the forms necessary to perform the QC on the slides/scenes. The user can rearrange, edit, and hide scenes with these forms.

class brain.forms.AnimalChoiceField(queryset, *, empty_label='---------', required=True, widget=None, label=None, initial=None, help_text='', to_field_name=None, limit_choices_to=None, blank=False, **kwargs)

Bases: ModelChoiceField

A simple class that returns the animal name.

label_from_instance(obj)

Convert objects into strings and generate the labels for the choices presented by this object. Subclasses can override this method to customize the display of the choices.

class brain.forms.AnimalForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: Form

Sets up fields for the select dropdown menu in forms. Animals are sorted by name.

class Meta

Bases: object

fields = ('prep_id',)
base_fields = {'prep_id': <django.forms.models.ModelChoiceField object>}
declared_fields = {'prep_id': <django.forms.models.ModelChoiceField object>}
property media

Return all media required to render the widgets on this form.

class brain.forms.TifInlineFormset(data=None, files=None, instance=None, save_as_new=False, prefix=None, queryset=None, **kwargs)

Bases: BaseInlineFormSet

This class defines the form for the subsets of scenes for a slide. This is where the work is done for rearranging and editing the scenes.

save_existing(form, instance, commit=True)

This is called when updating an instance of the inline tifs associated with a slide. The only thing to update is the scene order in case a user changes a number in the scene number text box. Note that the tifs in the form are only with channel 1, but if we reorder the scenes, we need to do it on all channels, not just channel 1.

Parameters:

  • form – Form object.

  • instance – slide CZI TIFF object.

  • commit – A boolean stating if the object should be committed.

brain.forms.create_scene(tifs, scene_index)

Helper method to create a scene.

Parameters:

  • tifs – A list of TIFFs.

  • scene_number – An integer used to find the nearest neighbor

brain.forms.find_closest_neighbor(slide, scene_index)
Helper method to get the nearest scene. Look first at the preceding tifs,

if nothing is there, go for the one just after.

Parameters:

  • slide – primary key of the slide

  • scene_number – scene number. 1 per set of 3 channels

Returns:

set of tifs

brain.forms.get_slide_channels(slide)
brain.forms.remove_scene(slide, deletes, scene_number)

Helper method to remove a scene.

Parameters:

  • slide – An integer primary key of the slide.

  • deletes – An integer defining how many scenes to delete.

  • scene_number – An integer used to find the nearest neighbor

brain.forms.repeat_scene(slide, inserts, scene_index)

Helper method to duplicate a scene.

Parameters:

  • slide – An integer primary key of the slide.

  • inserts – An integer defining how many scenes to insert.

  • scene_number – An integer used to find the nearest neighbor

brain.forms.save_slide_model(self, request, obj, form, change)

This method overrides the slide save method.

Parameters:

  • request – The HTTP request.

  • obj – The slide object.

  • form – The form object.

  • change – unused variable, shows if the form has changed.

brain.forms.scene_reorder(slide)

Helper method to reorder a set of scenes.

Parameters:

slide – An integer for the primary key of the slide.

brain.forms.set_end(slide, scene_number)

Helper method to set a scene as the very last one in a brain.

Parameters:

  • slide – An integer for the primary key of the slide.

  • scene_number – An integer used to find the nearest neighbor.

brain.forms.set_scene_active_inactive(slide, scene_index, active)

Helper method to set a scene as active or inactive.

Parameters:

  • slide – An integer for the primary key of the slide.

  • scene_number – An integer used to find the nearest neighbor.

  • active – A boolean defining whether to set the scene active or inactive