Breaking changes for 0.3.0: str_subset, process_1_serie, fluidimage.p…

…iv, params.series for works

doc/examples/bos_with_topology.py

@@ -4,7 +4,7 @@
 params = TopologyBOS.create_default_params()
 
 params.images.path = get_path_image_samples() / "Karman/Images"
-params.images.str_slice = "1:3"
+params.images.str_subset = "1:3"
 
 params.piv0.shape_crop_im0 = 32
 params.multipass.number = 2

doc/examples/experimental/image2image_await.py

@@ -16,7 +16,7 @@
 params.saving.postfix = "await_im2im_recompute"
 
 
-params.im2im = "fluidimage.preproc.image2image.im2im_func_example"
+params.im2im = "fluidimage.image2image.im2im_func_example"
 topology = TopologyImage2Image(params, logging_level="info")
 image2image.complete_im2im_params_with_default(params)
 

doc/examples/experimental/old_piv_recompute.py

@@ -1,8 +1,8 @@
 import os
 
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
-params = TopologyPIV.create_default_params()
+params = Topology.create_default_params()
 
 params.series.path = "../../../image_samples/Karman/Images3"
 params.series.ind_start = 1
@@ -14,7 +14,7 @@
 params.saving.how = "recompute"
 params.saving.postfix = "old_piv"
 
-topology = TopologyPIV(params, logging_level="info")
+topology = Topology(params, logging_level="info")
 # topology.make_code_graphviz('topo.dot')
 
 topology.compute()

doc/examples/experimental/piv_complete.py

@@ -1,9 +1,9 @@
 from fluidimage.experimental.executors.executor_await import (
     ExecutorAwaitMultiprocs,
 )
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
-params = TopologyPIV.create_default_params()
+params = Topology.create_default_params()
 
 params.series.path = "../../../image_samples/Karman/Images2"
 params.series.ind_start = 1
@@ -18,7 +18,7 @@
 params.saving.postfix = "piv_complete"
 
 
-topology = TopologyPIV(params, logging_level="debug")
+topology = Topology(params, logging_level="debug")
 # topology.make_code_graphviz('topo.dot')
 
 topology.compute(executer=ExecutorAwaitMultiprocs(topology), sequential=True)

doc/examples/experimental/piv_trio.py

@@ -2,10 +2,10 @@
 
 from fluidimage.experimental.no_topology_computations.base_trio import BaseAsync
 from fluidimage.experimental.no_topology_computations.piv_trio import PivTrio
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 from fluidimage.works.piv import multipass
 
-params = TopologyPIV.create_default_params()
+params = Topology.create_default_params()
 
 params.series.path = "../../../image_samples/Karman/Images3"
 

doc/examples/my_example_im2im.py

@@ -4,6 +4,7 @@
 """
 
 
-def im2im(im):
+def im2im(im_path):
+    im, path = im_path
     print("in the function im2im...")
-    return 2 * im
+    return 2 * im, path

doc/examples/my_example_im2im_class.py

@@ -9,6 +9,7 @@ def __init__(self, arg0, arg1):
         self.arg0 = arg0
         self.arg1 = arg1
 
-    def calcul(self, image):
+    def calcul(self, image_path):
+        image, path = image_path
         print(f"in the function Im2Im.calcul (arg0={self.arg0})...")
-        return 2 * image
+        return 2 * image, path

doc/examples/piv_as_real/job_piv.py

@@ -15,7 +15,7 @@
 
 import params_piv
 
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
 
 def main(args):
@@ -26,7 +26,7 @@ def main(args):
         postfix_out=args.postfix_out,
     )
 
-    topology = TopologyPIV(params, nb_max_workers=int(args.nb_cores))
+    topology = Topology(params, nb_max_workers=int(args.nb_cores))
     topology.compute(sequential=args.seq)
 
 

doc/examples/piv_as_real/params_piv.py

@@ -11,7 +11,7 @@
 
 from glob import glob
 
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
 
 def get_path(iexp):
@@ -27,7 +27,7 @@ def make_params_piv(
     if postfix_in is not None and postfix_in != "":
         path += "." + postfix_in
 
-    params = TopologyPIV.create_default_params()
+    params = Topology.create_default_params()
     params.series.path = path
 
     print("path", path)
@@ -38,9 +38,9 @@ def make_params_piv(
 
     pathim = paths[0]
     if pathim.endswith("a.png") or pathim.endswith("b.png"):
-        params.series.strcouple = "i, 0:2"
+        params.series.str_subset = "i, 0:2"
     else:
-        params.series.strcouple = "i:i+2"
+        params.series.str_subset = "i:i+2"
     params.series.ind_start = 60
     params.series.ind_stop = None
 

doc/examples/piv_as_real/params_pre.py

@@ -41,9 +41,9 @@ def make_params_pre(iexp, savinghow="recompute", postfix_out="pre"):
     pathim = paths[0]
     double_frame = pathim.endswith("a.png") or pathim.endswith("b.png")
     if double_frame:
-        params.preproc.series.strcouple = "i:i+1, 0"
+        params.preproc.series.str_subset = "i:i+1, 0"
     else:
-        params.preproc.series.strcouple = "i:i+1"
+        params.preproc.series.str_subset = "i:i+1"
 
     params.preproc.series.ind_start = 60
     params.preproc.series.ind_stop = 62
@@ -63,8 +63,8 @@ def make_params_pre(iexp, savinghow="recompute", postfix_out="pre"):
     if double_frame:
         # for 'b.png' images
         params2 = deepcopy(params)
-        params2.preproc.series.strcouple = (
-            params.preproc.series.strcouple[:-1] + "1"
+        params2.preproc.series.str_subset = (
+            params.preproc.series.str_subset[:-1] + "1"
         )
         return [params, params2]
     else:

doc/examples/piv_as_real/try_piv.py

@@ -16,7 +16,7 @@
 import params_piv
 
 from fluidimage import SeriesOfArrays
-from fluidimage.works.piv import WorkPIV
+from fluidimage.piv import WorkPIV
 
 try:
     reload
@@ -32,16 +32,8 @@
 
 work = WorkPIV(params=params)
 
-pathin = params.series.path
-
-series = SeriesOfArrays(
-    pathin, params.series.strcouple, ind_start=params.series.ind_start
-)
-
 # c060a.png and c060b.png
-serie = series.get_serie_from_index(params.series.ind_start)
-
-piv = work.calcul(serie)
+piv = work.process_1_serie(params.series.ind_start)
 
 # piv.piv0.display(show_interp=True, scale=0.05, show_error=True)
 

doc/examples/piv_try_params.py

@@ -1,7 +1,6 @@
 """To be run in IPython to find a good set of parameters"""
 
-from fluidimage import SeriesOfArrays
-from fluidimage.works.piv import WorkPIV
+from fluidimage.piv import WorkPIV
 
 params = WorkPIV.create_default_params()
 
@@ -15,15 +14,14 @@
 
 params.mask.strcrop = "30:250, 100:"
 
-work = WorkPIV(params=params)
-
 path = "../../image_samples/Oseen/Images"
 # path = '../../image_samples/Karman/Images'
-series = SeriesOfArrays(path, "i+1:i+3")
-# we select the serie corresponding to i = 0
-serie = series.get_serie_from_index(0)
+params.series.path = path
+params.series.str_subset = "i+1:i+3"
+
+work = WorkPIV(params=params)
 
-piv = work.calcul(serie)
+piv = work.process_1_serie()
 
 # piv.display(show_interp=True, scale=0.3, show_error=True)
 piv.display(show_interp=False, scale=1, show_error=True)

doc/examples/piv_try_params_with_im2im_preproc.py

@@ -1,8 +1,7 @@
-from fluidimage import SeriesOfArrays
-from fluidimage.preproc.image2image import apply_im2im_filter
-from fluidimage.works.piv import WorkPIV
+from fluidimage.image2image import apply_im2im_filter
+from fluidimage.piv import Work
 
-params = WorkPIV.create_default_params()
+params = Work.create_default_params()
 
 params.multipass.number = 2
 params.multipass.use_tps = True
@@ -14,12 +13,14 @@
 
 params.mask.strcrop = "30:250, 100:"
 
-work = WorkPIV(params=params)
-
 path = "../../image_samples/Oseen/Images"
 # path = '../../image_samples/Karman/Images'
-series = SeriesOfArrays(path, "i+1:i+3")
-serie = series.get_serie_from_index(0)
+params.series.path = path
+params.series.str_subset = "i+1:i+3"
+
+work = Work(params=params)
+
+serie = work.get_serie()
 
 # "image to image" filter
 serie = apply_im2im_filter(serie, im2im="my_example_im2im.im2im")

doc/examples/piv_with_topo_and_preproc.py

@@ -1,7 +1,7 @@
 from fluidimage import get_path_image_samples
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
-params = TopologyPIV.create_default_params()
+params = Topology.create_default_params()
 
 params.series.path = get_path_image_samples() / "Karman/Images"
 params.series.ind_start = 1
@@ -22,7 +22,7 @@
 # Here the "image to image" function will be imported with the statement
 # `from my_example_im2im import im2im`
 
-topology = TopologyPIV(params, logging_level="info")
+topology = Topology(params, logging_level="info")
 
 # To produce a graph of the topology
 topology.make_code_graphviz("topo.dot")

doc/examples/piv_with_topo_and_preproc_class.py

@@ -1,7 +1,7 @@
 from fluidimage import get_path_image_samples
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
-params = TopologyPIV.create_default_params()
+params = Topology.create_default_params()
 
 params.series.path = get_path_image_samples() / "Karman/Images"
 params.series.ind_start = 1
@@ -23,7 +23,7 @@
 # Here, the class will be imported with the statement
 # `from my_example_im2im_class import Im2Im`
 
-topology = TopologyPIV(params, logging_level="info")
+topology = Topology(params, logging_level="info")
 
 # To produce a graph of the topology
 topology.make_code_graphviz("topo.dot")

doc/examples/piv_complete.py → doc/examples/piv_with_topo_complete.py

@@ -1,8 +1,8 @@
 import os
 
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
-params = TopologyPIV.create_default_params()
+params = Topology.create_default_params()
 
 params.series.path = "../../image_samples/Karman/Images"
 params.series.ind_start = 1
@@ -16,7 +16,7 @@
 params.saving.how = "complete"
 params.saving.postfix = "piv_complete"
 
-topology = TopologyPIV(params, logging_level="info")
+topology = Topology(params, logging_level="info")
 # topology.make_code_graphviz('topo.dot')
 
 topology.compute()

doc/examples/piv_with_topology.py

@@ -1,7 +1,7 @@
 from fluidimage import get_path_image_samples
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
-params = TopologyPIV.create_default_params()
+params = Topology.create_default_params()
 
 params.series.path = get_path_image_samples() / "Karman/Images"
 params.series.ind_start = 1
@@ -16,7 +16,7 @@
 # params.saving.how = 'complete'
 params.saving.postfix = "piv_example"
 
-topology = TopologyPIV(params, logging_level="info")
+topology = Topology(params, logging_level="info")
 
 # To produce a graph of the topology
 # topology.make_code_graphviz('topo.dot')

doc/examples/pivchallenge/bench_piv_2005C.py

@@ -4,14 +4,14 @@
 
 from path_images import get_path
 
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
 path = os.path.join(get_path("2005C"), "c*.bmp")
 
-params = TopologyPIV.create_default_params()
+params = Topology.create_default_params()
 
 params.series.path = path
-params.series.strcouple = "i, 0:2"
+params.series.str_subset = "i, 0:2"
 # params.series.ind_start = 48
 params.series.ind_stop = 20
 
@@ -28,7 +28,7 @@
 
 params.saving.how = "recompute"
 
-topology = TopologyPIV(params)
+topology = Topology(params)
 
 serie = topology.series.serie
 

doc/examples/pivchallenge/piv_2001A_topology.py

@@ -2,14 +2,14 @@
 
 from path_images import get_path
 
-from fluidimage.topologies.piv import TopologyPIV
+from fluidimage.piv import Topology
 
-params = TopologyPIV.create_default_params()
+params = Topology.create_default_params()
 
 path = os.path.join(get_path("2001A"), "A*")
 
 params.series.path = path
-params.series.strcouple = "i, 1:3"
+params.series.str_subset = "i, 1:3"
 params.series.ind_start = 1
 
 params.piv0.shape_crop_im0 = 32
@@ -19,7 +19,7 @@
 
 params.saving.how = "recompute"
 
-topology = TopologyPIV(params)
+topology = Topology(params)
 
 serie = topology.series.serie
 

doc/examples/pivchallenge/piv_2001A_work.py

@@ -3,7 +3,7 @@
 from path_images import get_path
 
 from fluidimage import SeriesOfArrays
-from fluidimage.works.piv import WorkPIV
+from fluidimage.piv import WorkPIV
 
 params = WorkPIV.create_default_params()