Remove accepted and rejected time series from the standard file outpu…

…ts and change denoised time series name (updated) (#1033)

* Fix time series

* Fix elif

* Apply new names to integration test output

* Update io unit test

* Update test io

* Update input reclassify_quiet_out.txt

* Changes in reclassify

* Ran black

* Update in cornell_three_echo_outputs.txt

* updated documentation

* Apply suggestions from code review

doc correction

Co-authored-by: Taylor Salo <tsalo90@gmail.com>

* Added comment for confusing code section

---------

Co-authored-by: Marta Arbizu Gómez <127724722+martaarbizu@users.noreply.github.com>
Co-authored-by: Eneko Uruñuela <e.urunuela@icloud.com>
Co-authored-by: Taylor Salo <tsalo90@gmail.com>

tedana/io.py

@@ -552,7 +552,8 @@ def write_split_ts(data, mmix, mask, comptable, io_generator, echo=0):
         Output directory.
     echo : :obj: `int`, optional
         Echo number to generate filenames, used by some verbose
-        functions. Default 0.
+        functions. Currently this is only not 0 when
+        io_generator.verbose==True. Default 0.
 
     Returns
     -------
@@ -562,13 +563,23 @@ def write_split_ts(data, mmix, mask, comptable, io_generator, echo=0):
     Generated Files
     ---------------
 
-    ============================    ============================================
-    Filename                        Content
-    ============================    ============================================
-    [prefix]Accepted_bold.nii.gz    High-Kappa time series.
-    [prefix]Rejected_bold.nii.gz    Low-Kappa time series.
-    [prefix]Denoised_bold.nii.gz    Denoised time series.
-    ============================    ============================================
+    =====================================    ============================================
+    Filename                                 Content
+    =====================================    ============================================
+    desc-denoised_bold.nii.gz                Denoised time series.
+
+    if io_generator.verbose==True
+    desc-optcomAccepted_bold.nii.gz          High-Kappa time series.
+    desc-optcomRejected_bold.nii.gz          Low-Kappa time series.
+
+    if echo>0
+    echo-[echo]_desc-Accepted_bold.nii.gz    High-Kappa timeseries for echo
+                                             number ``echo``.
+    echo-[echo]_desc-Rejected_bold.nii.gz    Low-Kappa timeseries for echo
+                                             number ``echo``.
+    echo-[echo]_desc-Denoised_bold.nii.gz    Denoised timeseries for echo
+                                             number ``echo``.
+    =====================================    ============================================
     """
     acc = comptable[comptable.classification == "accepted"].index.values
     rej = comptable[comptable.classification == "rejected"].index.values
@@ -577,17 +588,23 @@ def write_split_ts(data, mmix, mask, comptable, io_generator, echo=0):
 
     if len(acc) != 0:
         if echo != 0:
+            # This outputs time series for a single echo
+            # In practice this only happens when verbose is true
+            # in io.writeresults_echoes. Neither this or the elif below
+            # are written out if verbose is not true
             fout = io_generator.save_file(hikts, "high kappa ts split img", echo=echo)
-        else:
+            LGR.info(f"Writing high-Kappa time series: {fout}")
+        elif io_generator.verbose:
             fout = io_generator.save_file(hikts, "high kappa ts img")
-        LGR.info(f"Writing high-Kappa time series: {fout}")
+            LGR.info(f"Writing high-Kappa time series: {fout}")
 
     if len(rej) != 0:
         if echo != 0:
             fout = io_generator.save_file(lowkts, "low kappa ts split img", echo=echo)
-        else:
+            LGR.info(f"Writing low-Kappa time series: {fout}")
+        elif io_generator.verbose:
             fout = io_generator.save_file(lowkts, "low kappa ts img")
-        LGR.info(f"Writing low-Kappa time series: {fout}")
+            LGR.info(f"Writing low-Kappa time series: {fout}")
 
     if echo != 0:
         fout = io_generator.save_file(dnts, "denoised ts split img", echo=echo)
@@ -623,19 +640,20 @@ def writeresults(ts, mask, comptable, mmix, io_generator):
     Generated Files
     ---------------
 
-    =========================================    =====================================
+    =========================================    ===========================================
     Filename                                     Content
-    =========================================    =====================================
-    desc-optcomAccepted_bold.nii.gz              High-Kappa time series.
-    desc-optcomRejected_bold.nii.gz              Low-Kappa time series.
-    desc-optcomDenoised_bold.nii.gz              Denoised time series.
+    =========================================    ===========================================
+    desc-denoised_bold.nii.gz              Denoised time series.
+
+    desc-optcomAccepted_bold.nii.gz              High-Kappa time series. (only with verbose)
+    desc-optcomRejected_bold.nii.gz              Low-Kappa time series. (only with verbose)
     desc-ICA_components.nii.gz                   Spatial component maps for all
                                                  components.
     desc-ICAAccepted_components.nii.gz           Spatial component maps for accepted
                                                  components.
     desc-ICAAccepted_stat-z_components.nii.gz    Z-normalized spatial component maps
                                                  for accepted components.
-    =========================================    =====================================
+    =========================================    ===========================================
     """
     acc = comptable[comptable.classification == "accepted"].index.values
     write_split_ts(ts, mmix, mask, comptable, io_generator)

tedana/resources/config/outputs.json

@@ -37,7 +37,7 @@
     },
     "denoised ts img": {
         "orig": "dn_ts_OC",
-        "bidsv1.5.0": "desc-optcomDenoised_bold"
+        "bidsv1.5.0": "desc-denoised_bold"
     },
     "high kappa ts img": {
         "orig": "hik_ts_OC",

tedana/tests/data/cornell_three_echo_outputs.txt

@@ -20,9 +20,7 @@ desc-PCA_metrics.tsv
 desc-PCA_mixing.tsv
 desc-PCA_stat-z_components.nii.gz
 desc-adaptiveGoodSignal_mask.nii.gz
-desc-optcomAccepted_bold.nii.gz
-desc-optcomDenoised_bold.nii.gz
-desc-optcomRejected_bold.nii.gz
+desc-denoised_bold.nii.gz
 desc-optcom_bold.nii.gz
 figures
 figures/carpet_optcom.svg

tedana/tests/data/fiu_four_echo_outputs.txt

@@ -28,7 +28,7 @@ sub-01_desc-limited_S0map.nii.gz
 sub-01_desc-limited_T2starmap.nii.gz
 sub-01_desc-optcomAcceptedMIRDenoised_bold.nii.gz
 sub-01_desc-optcomAccepted_bold.nii.gz
-sub-01_desc-optcomDenoised_bold.nii.gz
+sub-01_desc-denoised_bold.nii.gz
 sub-01_desc-optcomMIRDenoised_bold.nii.gz
 sub-01_desc-optcomNoGlobalSignal_bold.nii.gz
 sub-01_desc-optcomRejected_bold.nii.gz

tedana/tests/data/nih_five_echo_outputs_verbose.txt

@@ -29,7 +29,7 @@ sub-01_desc-adaptiveGoodSignal_mask.nii.gz
 sub-01_desc-limited_S0map.nii.gz
 sub-01_desc-limited_T2starmap.nii.gz
 sub-01_desc-optcomAccepted_bold.nii.gz
-sub-01_desc-optcomDenoised_bold.nii.gz
+sub-01_desc-denoised_bold.nii.gz
 sub-01_desc-optcom_whitened_bold.nii.gz
 sub-01_desc-optcomRejected_bold.nii.gz
 sub-01_desc-optcom_bold.nii.gz

tedana/tests/data/reclassify_debug_out.txt

@@ -9,7 +9,6 @@ sub-testymctestface_dataset_description.json
 sub-testymctestface_dn_ts_OC.nii.gz
 sub-testymctestface_dn_ts_OC_MIR.nii.gz
 sub-testymctestface_feats_OC2.nii.gz
-sub-testymctestface_hik_ts_OC.nii.gz
 sub-testymctestface_hik_ts_OC_MIR.nii.gz
 sub-testymctestface_ica_components.nii.gz
 sub-testymctestface_ica_cross_component_metrics.json
@@ -21,6 +20,5 @@ sub-testymctestface_ica_mir_mixing.tsv
 sub-testymctestface_ica_mixing.tsv
 sub-testymctestface_ica_orth_mixing.tsv
 sub-testymctestface_ica_status_table.tsv
-sub-testymctestface_lowk_ts_OC.nii.gz
 sub-testymctestface_registry.json
 sub-testymctestface_sphis_hik.nii.gz

tedana/tests/data/reclassify_no_bold.txt

@@ -6,8 +6,7 @@ desc-ICA_decomposition.json
 desc-ICA_mixing.tsv
 desc-ICA_stat-z_components.nii.gz
 desc-ICA_status_table.tsv
-desc-optcomDenoised_bold.nii.gz
-desc-optcomRejected_bold.nii.gz
+desc-denoised_bold.nii.gz
 desc-tedana_metrics.json
 desc-tedana_metrics.tsv
 desc-tedana_registry.json

tedana/tests/data/reclassify_quiet_out.txt

@@ -8,9 +8,7 @@ desc-ICA_decomposition.json
 desc-ICA_mixing.tsv
 desc-ICA_stat-z_components.nii.gz
 desc-ICA_status_table.tsv
-desc-optcomAccepted_bold.nii.gz
-desc-optcomDenoised_bold.nii.gz
-desc-optcomRejected_bold.nii.gz
+desc-denoised_bold.nii.gz
 desc-tedana_metrics.json
 desc-tedana_metrics.tsv
 desc-tedana_registry.json

tedana/tests/data/reclassify_run_twice.txt

@@ -8,9 +8,7 @@ desc-ICA_decomposition.json
 desc-ICA_mixing.tsv
 desc-ICA_stat-z_components.nii.gz
 desc-ICA_status_table.tsv
-desc-optcomAccepted_bold.nii.gz
-desc-optcomDenoised_bold.nii.gz
-desc-optcomRejected_bold.nii.gz
+desc-denoised_bold.nii.gz
 desc-tedana_metrics.json
 desc-tedana_metrics.tsv
 desc-tedana_registry.json

tedana/tests/test_io.py

@@ -142,6 +142,7 @@ def test_smoke_write_split_ts():
     classification = np.random.choice(["accepted", "rejected", "ignored"], n_components)
     df_data = np.column_stack((component, metric, classification))
     comptable = pd.DataFrame(df_data, columns=["component", "metric", "classification"])
+    io_generator.verbose = True
 
     me.write_split_ts(data, mmix, mask, comptable, io_generator)
 
@@ -153,6 +154,17 @@ def test_smoke_write_split_ts():
         # remove all files generated
         os.remove(filename)
 
+    io_generator.verbose = False
+
+    me.write_split_ts(data, mmix, mask, comptable, io_generator)
+
+    # TODO: midk_ts.nii is never generated?
+    fn = io_generator.get_name
+    split = "denoised ts img"
+    fname = fn(split)
+    # remove all files generated
+    os.remove(fname)
+
 
 def test_smoke_filewrite():
     """