Add prefix to all output files

tedana/io.py

@@ -131,7 +131,7 @@ def __init__(
         self.convention = convention
         self.out_dir = op.abspath(out_dir)
         self.figures_dir = op.join(out_dir, "figures")
-        self.prefix = prefix + "_" if prefix != "" else ""
+        self.prefix = _infer_prefix(prefix)
         self.overwrite = overwrite
         self.verbose = verbose
         self.registry = {}
@@ -920,3 +920,9 @@ def fname_to_component_list(fname: str) -> List[int]:
     with open(fname, "r") as fp:
         contents = fp.read()
         return str_to_component_list(contents)
+
+
+def _infer_prefix(prefix):
+    """Determine the appropriate prefix for output files."""
+    prefix = prefix + "_" if (prefix != "" and not prefix.endswith("_")) else prefix
+    return prefix

tedana/reporting/data/html/report_body_template.html

@@ -158,44 +158,16 @@
     border-radius: 5px;
   }
 </style>
-<script language="javascript">
-  function updateCarpetPlot(name) {
-    if (name == "optcom") {
-      document.getElementById("imgCarpetPlot").src =
-        "./figures/carpet_optcom.svg";
-    } else if (name == "denoised") {
-      document.getElementById("imgCarpetPlot").src =
-        "./figures/carpet_denoised.svg";
-    } else if (name == "accepted") {
-      document.getElementById("imgCarpetPlot").src =
-        "./figures/carpet_accepted.svg";
-    } else if (name == "rejected") {
-      document.getElementById("imgCarpetPlot").src =
-        "./figures/carpet_rejected.svg";
-    } else if (name == "denoised_mir") {
-      document.getElementById("imgCarpetPlot").src =
-        "./figures/carpet_denoised_mir.svg";
-    } else if (name == "accepted_mir") {
-      document.getElementById("imgCarpetPlot").src =
-        "./figures/carpet_accepted_mir.svg";
-    } else if (name == "optcom_nogsr") {
-      document.getElementById("imgCarpetPlot").src =
-        "./figures/carpet_optcom_nogsr.svg";
-    }
-  }
-</script>
-<div class="report">
-  <div class="content">
-    <h1>ICA components</h1>
-    $content
-  </div>
-  <div class="carpet-plots">
-    <h1>Carpet plots</h1>
-    <div class="carpet-wrapper">
-      <div class="carpet-buttons">$buttons</div>
-      <div class="carpet-plots-image">
-        <img id="imgCarpetPlot" src="./figures/carpet_optcom.svg" />
-      </div>
+<div class="content">
+  <h1>ICA components</h1>
+  $content
+</div>
+<div class="carpet-plots">
+  <h1>Carpet plots</h1>
+  <div class="carpet-wrapper">
+    <div class="carpet-buttons">$buttons</div>
+    <div class="carpet-plots-image">
+      <img id="imgCarpetPlot" src="$initialCarpet" />
     </div>
   </div>
   <div class="info">
@@ -211,4 +183,30 @@ <h1>References</h1>
   </div>
 </div>
 
+<script type="text/javascript">
+  function updateCarpetPlot(name) {
+    // Create variable to hold the image source
+    let carpetPlot = "./figures/$prefix";
+
+    if (name == "optcom") {
+      carpetPlot += "carpet_optcom.svg";
+    } else if (name == "denoised") {
+      carpetPlot += "carpet_denoised.svg";
+    } else if (name == "accepted") {
+      carpetPlot += "carpet_accepted.svg";
+    } else if (name == "rejected") {
+      carpetPlot += "carpet_rejected.svg";
+    } else if (name == "denoised_mir") {
+      carpetPlot += "carpet_denoised_mir.svg";
+    } else if (name == "accepted_mir") {
+      carpetPlot += "carpet_accepted_mir.svg";
+    } else if (name == "optcom_nogsr") {
+      carpetPlot += "carpet_optcom_nogsr.svg";
+    }
+
+    // Update the image source
+    document.getElementById("imgCarpetPlot").src = carpetPlot;
+  }
+</script>
+
 $javascript

tedana/reporting/dynamic_figures.py

@@ -27,7 +27,7 @@
 
         // Image Below Plots
         div.text = ""
-        var line = "<span><img src='./figures/comp_"+selected_padded_forIMG+".png'" +
+        var line = "<span><img src='./figures/"+prefix+"comp_"+selected_padded_forIMG+".png'" +
             " alt='Component Map'><span>\\n";
         console.log('Linea: ' + line)
         var text = div.text.concat(line);
@@ -375,6 +375,7 @@ def _tap_callback(comptable_cds, div_content, io_generator):
             source_comp_table=comptable_cds,
             div=div_content,
             outdir=io_generator.out_dir,
+            prefix=io_generator.prefix,
         ),
         code=tap_callback_jscode,
     )

tedana/reporting/html_report.py

@@ -15,25 +15,25 @@
 LGR = logging.getLogger("GENERAL")
 
 
-def _generate_buttons(out_dir):
+def _generate_buttons(out_dir, io_generator):
     resource_path = Path(__file__).resolve().parent.joinpath("data", "html")
 
     images_list = [img for img in os.listdir(out_dir) if ".svg" in img]
     optcom_nogsr_disp = "none"
     optcom_name = ""
-    if "carpet_optcom_nogsr.svg" in images_list:
+    if f"{io_generator.prefix}carpet_optcom_nogsr.svg" in images_list:
         optcom_nogsr_disp = "block"
         optcom_name = "before MIR"
 
     denoised_mir_disp = "none"
     denoised_name = ""
-    if "carpet_denoised_mir.svg" in images_list:
+    if f"{io_generator.prefix}carpet_denoised_mir.svg" in images_list:
         denoised_mir_disp = "block"
         denoised_name = "before MIR"
 
     accepted_mir_disp = "none"
     accepted_name = ""
-    if "carpet_accepted_mir.svg" in images_list:
+    if f"{io_generator.prefix}carpet_accepted_mir.svg" in images_list:
         accepted_mir_disp = "block"
         accepted_name = "before MIR"
 
@@ -54,7 +54,7 @@ def _generate_buttons(out_dir):
     return buttons_html
 
 
-def _update_template_bokeh(bokeh_id, info_table, about, references, bokeh_js, buttons):
+def _update_template_bokeh(bokeh_id, about, prefix, references, bokeh_js, buttons):
     """
     Populate a report with content.
 
@@ -66,6 +66,8 @@ def _update_template_bokeh(bokeh_id, info_table, about, references, bokeh_js, bu
         HTML div created by _generate_info_table()
     about : str
         Reporting information for a given run
+    prefix : str
+        Prefix for the outputted figures
     references : str
         BibTeX references associated with the reporting information
     bokeh_js : str
@@ -78,14 +80,18 @@ def _update_template_bokeh(bokeh_id, info_table, about, references, bokeh_js, bu
     """
     resource_path = Path(__file__).resolve().parent.joinpath("data", "html")
 
+    # Initial carpet plot (default one)
+    initial_carpet = f"./figures/{prefix}carpet_optcom.svg"
+
     body_template_name = "report_body_template.html"
     body_template_path = resource_path.joinpath(body_template_name)
     with open(str(body_template_path), "r") as body_file:
         body_tpl = Template(body_file.read())
     body = body_tpl.substitute(
         content=bokeh_id,
-        info=info_table,
         about=about,
+        prefix=prefix,
+        initialCarpet=initial_carpet,
         references=references,
         javascript=bokeh_js,
         buttons=buttons,
@@ -257,13 +263,13 @@ def get_elbow_val(elbow_prefix):
     kr_script, kr_div = embed.components(app)
 
     # Generate html of buttons (only for images that were generated)
-    buttons_html = _generate_buttons(opj(io_generator.out_dir, "figures"))
+    buttons_html = _generate_buttons(opj(io_generator.out_dir, "figures"), io_generator)
 
     # Read in relevant methods
-    with open(opj(io_generator.out_dir, "report.txt"), "r+") as f:
+    with open(opj(io_generator.out_dir, f"{io_generator.prefix}report.txt"), "r+") as f:
         about = f.read()
 
-    with open(opj(io_generator.out_dir, "references.bib"), "r") as f:
+    with open(opj(io_generator.out_dir, f"{io_generator.prefix}references.bib"), "r") as f:
         references = f.read()
 
     # Read info table
@@ -278,9 +284,10 @@ def get_elbow_val(elbow_prefix):
         info_table=info_table,
         about=about,
         references=references,
+        prefix=io_generator.prefix,
         bokeh_js=kr_script,
         buttons=buttons_html,
     )
     html = _save_as_html(body)
-    with open(opj(io_generator.out_dir, "tedana_report.html"), "wb") as f:
+    with open(opj(io_generator.out_dir, f"{io_generator.prefix}tedana_report.html"), "wb") as f:
         f.write(html.encode("utf-8"))

tedana/reporting/static_figures.py

@@ -41,7 +41,15 @@ def _trim_edge_zeros(arr):
     return arr[bounding_box]
 
 
-def carpet_plot(optcom_ts, denoised_ts, hikts, lowkts, mask, io_generator, gscontrol=None):
+def carpet_plot(
+    optcom_ts,
+    denoised_ts,
+    hikts,
+    lowkts,
+    mask,
+    io_generator,
+    gscontrol=None,
+):
     """Generate a set of carpet plots for the combined and denoised data.
 
     Parameters
@@ -74,7 +82,9 @@ def carpet_plot(optcom_ts, denoised_ts, hikts, lowkts, mask, io_generator, gscon
         title="Optimally Combined Data",
     )
     fig.tight_layout()
-    fig.savefig(os.path.join(io_generator.out_dir, "figures", "carpet_optcom.svg"))
+    fig.savefig(
+        os.path.join(io_generator.out_dir, "figures", f"{io_generator.prefix}carpet_optcom.svg")
+    )
 
     fig, ax = plt.subplots(figsize=(14, 7))
     plotting.plot_carpet(
@@ -85,7 +95,9 @@ def carpet_plot(optcom_ts, denoised_ts, hikts, lowkts, mask, io_generator, gscon
         title="Denoised Data",
     )
     fig.tight_layout()
-    fig.savefig(os.path.join(io_generator.out_dir, "figures", "carpet_denoised.svg"))
+    fig.savefig(
+        os.path.join(io_generator.out_dir, "figures", f"{io_generator.prefix}carpet_denoised.svg")
+    )
 
     fig, ax = plt.subplots(figsize=(14, 7))
     plotting.plot_carpet(
@@ -96,7 +108,9 @@ def carpet_plot(optcom_ts, denoised_ts, hikts, lowkts, mask, io_generator, gscon
         title="High-Kappa Data",
     )
     fig.tight_layout()
-    fig.savefig(os.path.join(io_generator.out_dir, "figures", "carpet_accepted.svg"))
+    fig.savefig(
+        os.path.join(io_generator.out_dir, "figures", f"{io_generator.prefix}carpet_accepted.svg")
+    )
 
     fig, ax = plt.subplots(figsize=(14, 7))
     plotting.plot_carpet(
@@ -107,7 +121,9 @@ def carpet_plot(optcom_ts, denoised_ts, hikts, lowkts, mask, io_generator, gscon
         title="Low-Kappa Data",
     )
     fig.tight_layout()
-    fig.savefig(os.path.join(io_generator.out_dir, "figures", "carpet_rejected.svg"))
+    fig.savefig(
+        os.path.join(io_generator.out_dir, "figures", f"{io_generator.prefix}carpet_rejected.svg")
+    )
 
     if (gscontrol is not None) and ("gsr" in gscontrol):
         optcom_with_gs_img = io_generator.get_name("has gs combined img")
@@ -120,7 +136,13 @@ def carpet_plot(optcom_ts, denoised_ts, hikts, lowkts, mask, io_generator, gscon
             title="Optimally Combined Data (Pre-GSR)",
         )
         fig.tight_layout()
-        fig.savefig(os.path.join(io_generator.out_dir, "figures", "carpet_optcom_nogsr.svg"))
+        fig.savefig(
+            os.path.join(
+                io_generator.out_dir,
+                "figures",
+                f"{io_generator.prefix}carpet_optcom_nogsr.svg",
+            )
+        )
 
     if (gscontrol is not None) and ("mir" in gscontrol):
         mir_denoised_img = io_generator.get_name("mir denoised img")
@@ -133,7 +155,13 @@ def carpet_plot(optcom_ts, denoised_ts, hikts, lowkts, mask, io_generator, gscon
             title="Denoised Data (Post-MIR)",
         )
         fig.tight_layout()
-        fig.savefig(os.path.join(io_generator.out_dir, "figures", "carpet_denoised_mir.svg"))
+        fig.savefig(
+            os.path.join(
+                io_generator.out_dir,
+                "figures",
+                f"{io_generator.prefix}carpet_denoised_mir.svg",
+            )
+        )
 
         mir_denoised_img = io_generator.get_name("ICA accepted mir denoised img")
         fig, ax = plt.subplots(figsize=(14, 7))
@@ -145,7 +173,13 @@ def carpet_plot(optcom_ts, denoised_ts, hikts, lowkts, mask, io_generator, gscon
             title="High-Kappa Data (Post-MIR)",
         )
         fig.tight_layout()
-        fig.savefig(os.path.join(io_generator.out_dir, "figures", "carpet_accepted_mir.svg"))
+        fig.savefig(
+            os.path.join(
+                io_generator.out_dir,
+                "figures",
+                f"{io_generator.prefix}carpet_accepted_mir.svg",
+            )
+        )
 
 
 def comp_figures(ts, mask, comptable, mmix, io_generator, png_cmap):
@@ -284,7 +318,7 @@ def comp_figures(ts, mask, comptable, mmix, io_generator, png_cmap):
 
         # Fix spacing so TR label does overlap with other plots
         allplot.subplots_adjust(hspace=0.4)
-        plot_name = "comp_{}.png".format(str(compnum).zfill(3))
+        plot_name = f"{io_generator.prefix}comp_{str(compnum).zfill(3)}.png"
         compplot_name = os.path.join(io_generator.out_dir, "figures", plot_name)
         plt.savefig(compplot_name)
         plt.close()
@@ -363,7 +397,7 @@ def pca_results(criteria, n_components, all_varex, io_generator):
     plt.legend()
 
     #  Save the plot
-    plot_name = "pca_criteria.png"
+    plot_name = f"{io_generator.prefix}pca_criteria.png"
     pca_criteria_name = os.path.join(io_generator.out_dir, "figures", plot_name)
     plt.savefig(pca_criteria_name)
     plt.close()
@@ -425,7 +459,7 @@ def pca_results(criteria, n_components, all_varex, io_generator):
     plt.legend()
 
     #  Save the plot
-    plot_name = "pca_variance_explained.png"
+    plot_name = f"{io_generator.prefix}pca_variance_explained.png"
     pca_variance_explained_name = os.path.join(io_generator.out_dir, "figures", plot_name)
     plt.savefig(pca_variance_explained_name)
     plt.close()