full offset (#225)

gelles-brandeis · Oct 25, 2021 · 24dcbf2 · 24dcbf2
1 parent 9643e5d
commit 24dcbf2
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Showing 2 changed files with 24 additions and 13 deletions.
diff --git a/tapqir/imscroll/glimpse_reader.py b/tapqir/imscroll/glimpse_reader.py
@@ -282,31 +282,28 @@ def read_glimpse(path, **kwargs):
             assert (target_xy[dtype][c] > 0.5 * P - 1).all()
             assert (target_xy[dtype][c] < 0.5 * P).all()
 
+    min_data = np.inf
     for dtype in data.keys():
         # concatenate channels
         data[dtype] = np.stack(data[dtype], -3)
         target_xy[dtype] = np.stack(target_xy[dtype], -2)
-        # convert data into torch tensor
+        min_data = min(min_data, data[dtype].min())
+        # convert data to torch tensor
         data[dtype] = torch.tensor(data[dtype])
         target_xy[dtype] = torch.tensor(target_xy[dtype])
 
     # process offset data
     offsets = OrderedDict(sorted(offsets.items()))
     offset_samples = np.array(list(offsets.keys()))
     offset_weights = np.array(list(offsets.values()))
+    # if data.min() is smaller than the smallest offset then
+    # add a single point to offset samples with that value - 1
+    if min_data <= offset_samples[0]:
+        offset_samples = np.insert(offset_samples, 0, min_data - 1)
+        offset_weights = np.insert(offset_weights, 0, 1)
+    # normalize weights
     offset_weights = offset_weights / offset_weights.sum()
-    # remove values from lower and upper 0.5 percentile
-    low_mask = offset_weights.cumsum() < 0.005
-    low_weights = offset_weights[low_mask].sum()
-    offset_samples = offset_samples[~low_mask]
-    offset_weights = offset_weights[~low_mask]
-    offset_weights[0] += low_weights
-    high_mask = offset_weights.cumsum() > 0.995
-    high_weights = offset_weights[high_mask].sum()
-    offset_samples = offset_samples[~high_mask]
-    offset_weights = offset_weights[~high_mask]
-    offset_weights[-1] += high_weights
-    # convert data into torch tensor
+    # convert data to torch tensor
     offset_samples = torch.tensor(offset_samples, dtype=torch.int)
     offset_weights = torch.tensor(offset_weights)
 

diff --git a/tapqir/main.py b/tapqir/main.py
@@ -166,12 +166,17 @@ def glimpse(
         for c in range(num_channels):
             if len(DEFAULTS["channels"]) < c + 1:
                 DEFAULTS["channels"].append(defaultdict(lambda: None))
+            else:
+                DEFAULTS["channels"][c] = defaultdict(
+                    lambda: None, DEFAULTS["channels"][c]
+                )
             keys = [
                 "name",
                 "glimpse-folder",
                 "ontarget-aoiinfo",
                 "offtarget-aoiinfo",
                 "driftlist",
+                "ontarget-labels",
             ]
             typer.echo(f"\nINPUTS FOR CHANNEL #{c}\n")
             for key in keys:
@@ -184,6 +189,15 @@ def glimpse(
                         if "offtarget-aoiinfo" in DEFAULTS["channels"][c]:
                             del DEFAULTS["channels"][c]["offtarget-aoiinfo"]
                         continue
+                elif key == "ontarget-labels":
+                    labels = typer.confirm(
+                        "Add on-target labels?",
+                        default=("ontarget-labels" in DEFAULTS["channels"][c]),
+                    )
+                    if not labels:
+                        if "ontarget-labels" in DEFAULTS["channels"][c]:
+                            del DEFAULTS["channels"][c]["ontarget-labels"]
+                        continue
                 DEFAULTS["channels"][c][key] = typer.prompt(
                     desc[key], default=DEFAULTS["channels"][c][key]
                 )