fix for command line

requirements.txt

@@ -3,7 +3,7 @@ setuptools>=70.3.0
 napari>=0.5.0
 
 torch>=2.3.0
-tardis_em>=0.2.8
+tardis_em>=0.2.9
 
 numpy>=2.0.0
 

setup.cfg

@@ -10,7 +10,7 @@ author_email = [email protected]
 license =  MIT
 license_files = LICENSE
 classifiers =
-    Development Status :: 4 - Beta
+    Development Status :: 5 - Production/Stable
     Framework :: napari
     Intended Audience :: Developers
     License :: OSI Approved :: BSD License

src/napari_tardis_em/_version.py

@@ -1 +1 @@
-version = "0.2.9"
+version = "0.2.10"

src/napari_tardis_em/viewers/viewer_actin_3d.py

@@ -232,6 +232,7 @@ def __init__(self, viewer_actin_3d: Viewer):
 
         self.export_command = QPushButton("Export command for high-throughput")
         self.export_command.setMinimumWidth(225)
+        self.export_command.clicked.connect(self.show_command)
 
         ###########################
         # Optional Actin  Filters #

src/napari_tardis_em/viewers/viewer_mem_2d.py

@@ -232,6 +232,7 @@ def __init__(self, viewer_mem_2d: Viewer):
 
         self.export_command = QPushButton("Export command for high-throughput")
         self.export_command.setMinimumWidth(225)
+        self.export_command.clicked.connect(self.show_command)
 
         #############################
         # Optional Membrane Filters #

src/napari_tardis_em/viewers/viewer_mem_3d.py

@@ -231,6 +231,7 @@ def __init__(self, viewer_mem_3d: Viewer):
 
         self.export_command = QPushButton("Export command for high-throughput")
         self.export_command.setMinimumWidth(225)
+        self.export_command.clicked.connect(self.show_command)
 
         """""" """""" """
            UI Setup

src/napari_tardis_em/viewers/viewer_mt_3d.py

@@ -232,6 +232,7 @@ def __init__(self, viewer_mt_3d: Viewer):
 
         self.export_command = QPushButton("Export command for high-throughput")
         self.export_command.setMinimumWidth(225)
+        self.export_command.clicked.connect(self.show_command)
 
         #################################
         # Optional Microtubules Filters #

src/napari_tardis_em/viewers/viewer_predict.py

@@ -246,6 +246,7 @@ def __init__(self, viewer_predict: Viewer):
 
         self.export_command = QPushButton("Export command for high-throughput")
         self.export_command.setMinimumWidth(225)
+        self.export_command.clicked.connect(self.show_command)
 
         #################################
         # Optional Filament Filters #
@@ -722,22 +723,21 @@ def predict_dist():
             worker.start()
 
     def show_command(self):
-        mask = "" if not bool(self.mask.checkState()) else "-ms True"
+        ms = "" if not bool(self.mask.checkState()) else "-ms True"
 
-        correct_px = (
+        px = (
             ""
             if self.correct_px.text() == "None"
             else f"-px {float(self.correct_px.text())} "
         )
+
         if self.px is not None:
-            correct_px = (
+            px = (
                 ""
                 if self.px == float(self.correct_px.text())
                 else f"-px {float(self.correct_px.text())} "
             )
 
-        px = "" if not bool(self.mask.checkState()) else "-ms True "
-
         ch = (
             ""
             if self.checkpoint.text() == "None"
@@ -777,7 +777,7 @@ def show_command(self):
         show_info(
             f"tardis_predict "
             f"-dir {self.out_} "
-            f"{mask}"
+            f"{ms}"
             f"{px}"
             f"{fi}"
             f"{it}"

src/napari_tardis_em/viewers/viewer_train.py

@@ -288,6 +288,10 @@ def __init__(self, viewer_train: Viewer):
         self.stop_button = QPushButton("Stop Training")
         self.stop_button.setMinimumWidth(225)
 
+        self.export_command = QPushButton("Export command for high-throughput")
+        self.export_command.setMinimumWidth(225)
+        self.export_command.clicked.connect(self.show_command)
+
         """""" """""" """
            UI Setup
         """ """""" """"""
@@ -325,6 +329,7 @@ def __init__(self, viewer_train: Viewer):
 
         layout.addRow("", self.train_button)
         layout.addRow("", self.stop_button)
+        layout.addRow("", self.export_command)
 
         self.setLayout(layout)
 
@@ -729,3 +734,118 @@ def show_validation(self, init_=False):
                 visibility=True,
                 range_=(0, 1),
             )
+
+    def show_command(self):
+        ps = ("" if self.patch_size.currentText() == "64"
+              else f"-ps {int(self.patch_size.currentText())} ")
+
+        px = ("" if self.pixel_size.text() == "None"
+              else f"-px {float(self.pixel_size.text())} ")
+
+        ms = ("" if not int(self.mask_size.text()) == 150
+              else f"-ms {int(self.mask_size.text())} ")
+
+        cnn = (
+            ""
+            if self.cnn_type.currentText() == "unet"
+            else f"-cnn {self.cnn_type.currentText()} "
+        )
+
+        co = (
+            "" if int(self.cnn_out_channel.text()) == 1
+            else f"-co {int(self.cnn_out_channel.text())} "
+        )
+
+        b = (
+            "" if int(self.batch_size.text()) == 25
+            else f"-b {int(self.batch_size.text())} "
+        )
+
+        cl = (
+            "" if int(self.cnn_layers.text()) == 5
+            else f"-cl {int(self.cnn_layers.text())} "
+        )
+
+        cm = (
+            "" if int(self.cnn_scaler.currentText()) == 32
+            else f"-cm {int(self.cnn_scaler.currentText())} "
+        )
+
+        if self.image_type.currentText() == "2D":
+            cs = (
+                "" if self.cnn_structure.text() == "gcl"
+                else f"-cs 2{self.cnn_structure.text()} "
+            )
+        else:
+            cs = (
+                "" if self.cnn_structure.text() == "gcl"
+                else f"-cs 3{self.cnn_structure.text()} "
+            )
+
+        ck = (
+            "" if int(self.cnn_kernel.text()) == 3
+            else f"-ck {int(self.cnn_kernel.text())} "
+        )
+
+        cp = (
+            "" if int(self.cnn_padding.text()) == 1
+            else f"-cp {int(self.cnn_padding.text())} "
+        )
+
+        cmpk = (
+            "" if int(self.cnn_max_pool.text()) == 2
+            else f"-cmpk {int(self.cnn_max_pool.text())} "
+        )
+
+        l = (
+            "" if self.loss_function.currentText() == "BCELoss"
+            else f"-l {self.loss_function.currentText()} "
+        )
+
+        lr = (
+            "" if float(self.learning_rate.text()) == 0.0005
+            else f"-lr {float(self.learning_rate.text())} "
+        )
+
+        e = (
+            "" if int(self.epoch.text()) == 10000
+            else f"-e {int(self.epoch.text())} "
+        )
+
+        es = (
+            "" if int(self.early_stop.text()) == 10000
+            else f"-es {int(self.early_stop.text())} "
+        )
+
+        dp = (
+            "" if float(self.dropout_rate.text()) == 0.5
+            else f"-dp {float(self.dropout_rate.text())} "
+        )
+
+        cch = (
+            "" if self.checkpoint_dir is None else
+            f"-cch {self.checkpoint_dir} "
+        )
+
+        show_info(
+            f"tardis_cnn_train "
+            f"-dir {self.out_} "
+            f"{ps}"
+            f"{px}"
+            f"{ms}"
+            f"{cnn}"
+            f"{co}"
+            f"{b}"
+            f"{cl}"
+            f"{cm}"
+            f"{cs}"
+            f"{cp}"
+            f"{cmpk}"
+            f"{l}"
+            f"{lr}"
+            f"{e}"
+            f"{es}"
+            f"{dp}"
+            f"{cch}"
+            f"-dv {self.device.currentText()}"
+        )