diff --git a/src/dcnum/feat/feat_background/base.py b/src/dcnum/feat/feat_background/base.py index ff8a333..96a376f 100644 --- a/src/dcnum/feat/feat_background/base.py +++ b/src/dcnum/feat/feat_background/base.py @@ -130,7 +130,7 @@ def get_ppid(self): """Return a unique background pipeline identifier The pipeline identifier is universally applicable and must - be backwards-compatible (future versions of dcevent will + be backwards-compatible (future versions of dcnum will correctly acknowledge the ID). The segmenter pipeline ID is defined as:: diff --git a/src/dcnum/feat/feat_texture/tex_all.py b/src/dcnum/feat/feat_texture/tex_all.py index 0d924e9..dfe8746 100644 --- a/src/dcnum/feat/feat_texture/tex_all.py +++ b/src/dcnum/feat/feat_texture/tex_all.py @@ -6,6 +6,34 @@ def haralick_texture_features( mask, image=None, image_bg=None, image_corr=None): + """Compute Haralick texture features + + The following texture features are excluded + + - feature 6 "Sum Average", which is equivalent to `2 * bright_bc_avg` + since dclab 0.44.0 + - feature 10 "Difference Variance", because it has a functional + dependency on the offset value and since we do background correction, + we are not interested in it + - feature 14, because nobody is using it, it is not understood by + everyone what it actually is, and it is computationally expensive. + + This leaves us with the following 11 texture features (22 if you count + avg and ptp): + https://earlglynn.github.io/RNotes/package/EBImage/Haralick-Textural-Features.html + + - 1. `tex_asm`: (1) Angular Second Moment + - 2. `tex_con`: (2) Contrast + - 3. `tex_cor`: (3) Correlation + - 4. `tex_var`: (4) Variance + - 5. `tex_idm`: (5) Inverse Difference Moment + - 6. `tex_sva`: (7) Sum Variance + - 7. `tex_sen`: (8) Sum Entropy + - 8. `tex_ent`: (9) Entropy + - 9. `tex_den`: (11) Difference Entropy + - 10. `tex_f12`: (12) Information Measure of Correlation 1 + - 11. `tex_f13`: (13) Information Measure of Correlation 2 + """ # make sure we have a boolean array mask = np.array(mask, dtype=bool) size = mask.shape[0] @@ -22,7 +50,6 @@ def haralick_texture_features( for ii in range(size): # Haralick texture features - # https://gitlab.gwdg.de/blood_data_analysis/dcevent/-/issues/20 # Preprocessing: # - create a copy of the array (don't edit `image_corr`) # - add grayscale values (negative values not supported) diff --git a/src/dcnum/feat/gate.py b/src/dcnum/feat/gate.py index 0dce235..198adbf 100644 --- a/src/dcnum/feat/gate.py +++ b/src/dcnum/feat/gate.py @@ -20,7 +20,7 @@ def __init__(self, data, *, Parameters ---------- data: .HDF5Data - dcevent data instance + dcnum data instance online_gates: bool set to True to enable gating with "online" gates stored in the input file; online gates are applied in real-time @@ -95,7 +95,7 @@ def get_ppid(self): """Return a unique gating pipeline identifier The pipeline identifier is universally applicable and must - be backwards-compatible (future versions of dcevent will + be backwards-compatible (future versions of dcnum will correctly acknowledge the ID). The gating pipeline ID is defined as:: diff --git a/src/dcnum/feat/queue_event_extractor.py b/src/dcnum/feat/queue_event_extractor.py index e532a86..7a860ab 100644 --- a/src/dcnum/feat/queue_event_extractor.py +++ b/src/dcnum/feat/queue_event_extractor.py @@ -266,7 +266,7 @@ def get_ppid(self): """Return a unique feature extractor pipeline identifier The pipeline identifier is universally applicable and must - be backwards-compatible (future versions of dcevent will + be backwards-compatible (future versions of dcnum will correctly acknowledge the ID). The feature extractor pipeline ID is defined as::