From 8899b01fe7c8538d89488489c6c2b4d286b095f1 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Fri, 22 Oct 2021 13:23:49 -0500
Subject: [PATCH 1/6] Update _solis.py

imports series working example
---
 WrightTools/data/_solis.py | 63 ++++++++++++++++++++++++++++----------
 1 file changed, 47 insertions(+), 16 deletions(-)

diff --git a/WrightTools/data/_solis.py b/WrightTools/data/_solis.py
index d77be5f35..2eb7a296b 100644
--- a/WrightTools/data/_solis.py
+++ b/WrightTools/data/_solis.py
@@ -30,7 +30,7 @@ def from_Solis(filepath, name=None, parent=None, verbose=True) -> Data:
     Parameters
     ----------
     filepath : path-like
-        Path to .txt file.
+        Path to file (should be .asc format).
         Can be either a local or remote file (http/ftp).
         Can be compressed with gz/bz2, decompression based on file name.
     name : string (optional)
@@ -61,15 +61,33 @@ def from_Solis(filepath, name=None, parent=None, verbose=True) -> Data:
     axis0 = []
     arr = []
     attrs = {}
-    while True:
+    for i in range(2):
         line = f.readline().strip()[:-1]
-        if len(line) == 0:
-            break
-        else:
-            line = line.split(",")
-            line = [float(x) for x in line]
-            axis0.append(line.pop(0))
-            arr.append(line)
+        line = [float(x) for x in line.split(",")]  # TODO: robust to space, tab, comma
+        axis0.append(line.pop(0))
+        arr.append(line)
+    axis0_increasing = axis0[1] - axis0[0] > 0
+
+    def get_frames(f, arr, axis0, increasing):
+        axis0_written = False
+        while True:
+            line = f.readline().strip()[:-1]
+            if len(line) == 0:
+                break
+            else:
+                line = [float(x) for x in line.split(",")]
+                # signature of new frames is restart of axis0
+                if not axis0_written and ((line[0] - axis0[-1] > 0) != increasing):
+                    axis0_written = True
+                if axis0_written:
+                    line.pop(0)
+                else:
+                    axis0.append(line.pop(0))
+                arr.append(line)
+        return arr, axis0
+
+    arr, axis0 = get_frames(f, arr, axis0, axis0_increasing)
+    nframes = len(arr) // len(axis0)
 
     i = 0
     while i < 3:
@@ -94,10 +112,7 @@ def from_Solis(filepath, name=None, parent=None, verbose=True) -> Data:
         data = Data(**kwargs)
     else:
         data = parent.create_data(**kwargs)
-    arr = np.array(arr)
-    arr /= float(attrs["Exposure Time (secs)"])
-    # signal has units of Hz because time normalized
-    arr = data.create_channel(name="signal", values=arr, signed=False, units="Hz")
+
     axis0 = np.array(axis0)
     if float(attrs["Grating Groove Density (l/mm)"]) == 0:
         xname = "xindex"
@@ -105,9 +120,25 @@ def from_Solis(filepath, name=None, parent=None, verbose=True) -> Data:
     else:
         xname = "wm"
         xunits = "nm"
-    data.create_variable(name=xname, values=axis0[:, None], units=xunits)
-    data.create_variable(name="yindex", values=np.arange(arr.shape[1])[None, :], units=None)
-    data.transform(data.variables[0].natural_name, "yindex")
+    axes = [xname, "yindex"]
+
+    if nframes == 1:
+        arr = np.array(arr)
+        data.create_variable(name=xname, values=axis0[:, None], units=xunits)
+        data.create_variable(name="yindex", values=np.arange(arr.shape[-1])[None, :], units=None)
+    else:
+        arr = np.array(arr).reshape(nframes, len(axis0), len(arr[0]))
+        data.create_variable(name="frame", values=np.arange(nframes)[:, None, None], units=None)
+        data.create_variable(name=xname, values=axis0[None, :, None], units=xunits)
+        data.create_variable(name="yindex", values=np.arange(arr.shape[-1])[None, None, :], units=None)
+        axes = ["frame"] + axes
+
+    data.transform(*axes)
+    print(f"arr.shape {arr.shape}")
+    print(f'nframes {nframes}')
+    arr /= float(attrs["Exposure Time (secs)"])
+    # signal has units of Hz because time normalized
+    data.create_channel(name="signal", values=arr, signed=False, units="Hz")
 
     for key, val in attrs.items():
         data.attrs[key] = val

From 1bee64cc9891ea5d6b57c251a6a23c7ac31bb7fd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 25 Oct 2021 18:03:16 +0000
Subject: [PATCH 2/6] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 WrightTools/data/_solis.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/WrightTools/data/_solis.py b/WrightTools/data/_solis.py
index 2eb7a296b..071812996 100644
--- a/WrightTools/data/_solis.py
+++ b/WrightTools/data/_solis.py
@@ -130,12 +130,14 @@ def get_frames(f, arr, axis0, increasing):
         arr = np.array(arr).reshape(nframes, len(axis0), len(arr[0]))
         data.create_variable(name="frame", values=np.arange(nframes)[:, None, None], units=None)
         data.create_variable(name=xname, values=axis0[None, :, None], units=xunits)
-        data.create_variable(name="yindex", values=np.arange(arr.shape[-1])[None, None, :], units=None)
+        data.create_variable(
+            name="yindex", values=np.arange(arr.shape[-1])[None, None, :], units=None
+        )
         axes = ["frame"] + axes
 
     data.transform(*axes)
     print(f"arr.shape {arr.shape}")
-    print(f'nframes {nframes}')
+    print(f"nframes {nframes}")
     arr /= float(attrs["Exposure Time (secs)"])
     # signal has units of Hz because time normalized
     data.create_channel(name="signal", values=arr, signed=False, units="Hz")

From b9e7a29b8c970d6c6a9e6eacfcf34fe25eb30775 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 25 Oct 2021 13:28:26 -0500
Subject: [PATCH 3/6] Update CHANGELOG.md

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c1d5bb8b4..c479ed549 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 
 ## [Unreleased]
 
+### Added
+- `data.from_Solis`: "kinetic series" acquisition type now supported.
+
 ## [3.4.1]
 
 ### Added

From 681422f06bb7c57fbdcf9388372a89fce13d3817 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 25 Oct 2021 13:35:09 -0500
Subject: [PATCH 4/6] Update _solis.py

refactor frame detection
---
 WrightTools/data/_solis.py | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/WrightTools/data/_solis.py b/WrightTools/data/_solis.py
index 071812996..372658100 100644
--- a/WrightTools/data/_solis.py
+++ b/WrightTools/data/_solis.py
@@ -61,14 +61,13 @@ def from_Solis(filepath, name=None, parent=None, verbose=True) -> Data:
     axis0 = []
     arr = []
     attrs = {}
-    for i in range(2):
-        line = f.readline().strip()[:-1]
-        line = [float(x) for x in line.split(",")]  # TODO: robust to space, tab, comma
-        axis0.append(line.pop(0))
-        arr.append(line)
-    axis0_increasing = axis0[1] - axis0[0] > 0
-
-    def get_frames(f, arr, axis0, increasing):
+
+    line0 = f.readline().strip()[:-1]
+    line0 = [float(x) for x in line0.split(",")]  # TODO: robust to space, tab, comma
+    axis0.append(line0.pop(0))
+    arr.append(line0)
+
+    def get_frames(f, arr, axis0):
         axis0_written = False
         while True:
             line = f.readline().strip()[:-1]
@@ -77,7 +76,7 @@ def get_frames(f, arr, axis0, increasing):
             else:
                 line = [float(x) for x in line.split(",")]
                 # signature of new frames is restart of axis0
-                if not axis0_written and ((line[0] - axis0[-1] > 0) != increasing):
+                if not axis0_written and (line[0] == axis0[0]):
                     axis0_written = True
                 if axis0_written:
                     line.pop(0)
@@ -86,7 +85,7 @@ def get_frames(f, arr, axis0, increasing):
                 arr.append(line)
         return arr, axis0
 
-    arr, axis0 = get_frames(f, arr, axis0, axis0_increasing)
+    arr, axis0 = get_frames(f, arr, axis0)
     nframes = len(arr) // len(axis0)
 
     i = 0
@@ -136,8 +135,6 @@ def get_frames(f, arr, axis0, increasing):
         axes = ["frame"] + axes
 
     data.transform(*axes)
-    print(f"arr.shape {arr.shape}")
-    print(f"nframes {nframes}")
     arr /= float(attrs["Exposure Time (secs)"])
     # signal has units of Hz because time normalized
     data.create_channel(name="signal", values=arr, signed=False, units="Hz")

From 1104177d2a40a9709a3f6adc015b41c241f09e58 Mon Sep 17 00:00:00 2001
From: Daniel Kohler <11864045+ddkohler@users.noreply.github.com>
Date: Mon, 25 Oct 2021 15:17:48 -0500
Subject: [PATCH 5/6] test

---
 WrightTools/datasets/Solis/kinetic.asc.gz | Bin 0 -> 2852 bytes
 tests/data/from_Solis.py                  |   9 +++++++++
 2 files changed, 9 insertions(+)
 create mode 100644 WrightTools/datasets/Solis/kinetic.asc.gz

diff --git a/WrightTools/datasets/Solis/kinetic.asc.gz b/WrightTools/datasets/Solis/kinetic.asc.gz
new file mode 100644
index 0000000000000000000000000000000000000000..84ea4de54cf7230a838c88869437da6eace0e919
GIT binary patch
literal 2852
zcmV+<3)}P`iwFoE5O-k$|7&S(Wprs{E@5+H0F7JQa@$A_eOHzKfsdXlJ4?{IH2s!!
zHkqldWHNDT_E}MAo3*s4k*Q=nQ~U4Rlz3?X2hBK6`Jz^{8x5R3IDqLg&o3!W+b`!&
zO6mLycly%37JLbR(~qIc`78_O3BRN8jeJP=V)!|qU61c!Z}kroGpFMsXqd16f0}C%
zP9oP&=<V&?4(xM2TL!O(>vzLiUARWa9!tYR=ChSp)Hs8%QaBIsk*D3Q{kNI4My~8k
z{7}YOyC3E=r@VlD%B=(&rQz7b8N0wZp}|tL*YWH+TN7KU1B10!jwTL#x!oO+ekK{)
z)2ns;OMaqE&cNO!ER-`t<b0-U)2)M3laq);JsD~N0ytG(uVRq7-g!w&6++?jGVM#j
z5aD@#wv{+oVSI-c6vRCbb3fl2gr)Wb9t!|$PBwGWaa7RcPVJ1u0?t!m8x!^*fLKF-
zc>F|`<VPObpKNIJ>k^R2aM>Yn&4IPfrq6_9hH>I_%yDb?>uh0tG=ve+;d4Puhr?QE
z2a$tZ93T&yvPE`n9fpyHso0|hu5(KZ&lcXqA?duPwO%oWkeXu{lE>3xyY{}|-WGnJ
z8%K1SDhHUWt>F}AbI`~-e0LJMhn*=$3D&EzT_1*%u@^nT5Z)!SIli3<+!>(s8ei){
zJP4N*0OW!VE)0jB0CW^n1ITNVmP$lXejyFN;(N%jH%U(-_4RDAwL!dc1fRK0iO9tu
zEmh3cDc}xoX$T#F`=JY$ul5A*rth_%YvketXu=uY0Xh=mdXh=Aml?P-gKEylA~QU$
zGh@fGK79%tn9ht{pG)kX&jj9dmOK-7z>6@3I|*DA+%>ECrJ|{PYBAOp*mVk_Q3qcl
zoQ^sjOAe%N(DZ!B0PO^L%+$@wuNz8@s|EQIxC7b6Ol0vx%eSS~vS6|dGAY|ZF%9V9
zUAsHL$rx=w*p3*uMgY^dXbF$XbpXR&BTTOdlX#0;E4-3FjPyNM^ffi|8waxS;cj)d
zI-wQ`6S}-3q?DW2?gTmu-j|tqZTNhhR5R~tQC*ym@+TU6+6nI;XX|wsqz9;gW3*Qq
zF`(>IX&hD<LUmwaLS{IZ<NSqzM4-VK`bvr;JLD!IgIOWQ5|J8+A6Rg5>+Ts6GaNsC
zr<2>j*b|hTbCY3e4c7rpx2{k^R0y-tUWx$<iRRo^UVnCPh-f(JM1&;gNN$KW6egY!
z?*s&2W4sXd6$j_om^ew7RF0IkCNvnOV>yJ-W=7IMM2Fr4j>Qs;4A|(<avfPxs?#p5
zdpV@Opv(@YCQ4Ke#TRfLlNKy-Iy2xmA`-;60z?%aHUo;wXF5~9*2(u7!~qncyx5G$
zo|?;$BxH97Z(A0>3#ekHmWZcQ@gVA!k#|MGL2i<xIN2o%D4B6zIZ<;b#Ve(j<&(5w
z#PT$Plgy<=@nA&X+_H=fa#%|{J0~`})8|Rba2V31U~Nme7=0X2)>BB@?7MTAYEWLL
z7@;Pb{HPhCt6MjZCP*T|rlqaf0Ii!)g`uN-0i;K@QJsMhxL|ut-PSPDcn&_AOo958
z;lT|f74`4}w!#M}q)gjLfwqO#rY|v86bvPoRBEuK314pGV#v=4D`VJ4Q7x}8m4bLP
zwPARb_JTUd!+}bhM>6CA-{UTzltY+c5>sAOy^d@vrLwlNHuF21)uIZZ10_2*QU1{>
z950rVPQ#+ohANGv&_<f02pyXw`6Tn!3fJSJ@)8u%$%+ZZ5H$QSOeYkakz$fo<`)y1
zU<Tt@TR-6HY5a!EV>k4GpDSGWoKSLAppHt5p}xj%Q5VWAwlbhq8|k}YUkFLz$HGWd
zBIDOPS6X1u$I2Ulr<{nogVfonbOA~weQ^|EJfN3^yC}j$``Rq}TJWi`W59%kz8_PY
zI-%Jq5Yeq-rG-xv=q{;Z>!`9y;Q5jGb3Iu{#S0gQ0mt$zH__mPu1ZCk&VCM8&m;s)
zIkcQP_P-FgU>(98rMZF%DG<txLZamVSy)2MCbT6>R8ZBbL4a`*G*s~5>V?|s0{elL
zuSL?Q0pAVx%+U45ln%bK)kFuB;JXCnsGK#zsDy+f1#Wdd0OF%EXzUUbwNmVsPO5We
z<%dE|#wH|F)y1G(YE%WH2(Mi=!_Hu56a)$YJ<f|1f@LsD3lJWS7`v>QYQBV`U?|}(
zaj4}HBt|J~hpH>ka^z43#@dLuH;xFeSdOZDz@p|TtfPe3^lcTBdC=mB%g9#U3(2-Q
z2l%KMkj9!;Xfza&h3&CU6>S$ohY{G})XSt~&Y{CmBMh5=jeC!Bsm0(L50YXXYUpL@
z#4>&r+Z`V)WV*>#KhUX{PN*}Z923;5e^>{X<wVv4V^?a8k`T#+DUYboGDya5WGMhM
zK<8yX-3e_~OayNiTux>8y0{tiS{hb$aUQDAc+_A>goL<B$quTXO#~Xd)q@->8pvMt
z)VimJ3UV4r%!swVnB{hdo33?V$QmJ{*3nGy7HI3H(r<W&3scG5C<)>sX@uGm($%e$
z+nL>aY&tUb<!~Px;m&EL#h~O(7aj14kS><W=14cC_YQZ%BHqU+H=o%;nv~a3@2AnI
z%35Qj1Y@*M<VGuguG$$RLJ(HcP{(;FtP3_W(P=4MrSEnLuSb$)zep$qhnHc7p{!)I
zN%IPX(OrV*6e+A{*LpS~0HO{fSjip;dTy1g@crbhis_F@3<g(pgP`tI+Z_HQ1v3>Q
z)W`_BabaZw^)>afdX7#8wj989o*^BGWD)U=_x3Sa9UpS^FFXi{&hU@0aH9e&x{%b>
zEm98>wKZs@=$4hCI}YVNF{%ez7@<&4fL_TQAXHu8Era{6aSARP)U|YAl*t_K=U>_S
z0KV-FryKgy^B*ld#2V>4P$we^i`<O*a?f?{V-)n$7_(K13r$tIVV`=xtoGlVO;aSB
z-Ph!E`BdB_;^Te2OMcxpNw!Qfx=HC~;gT%PXg<5E@0;(NLy`Pm9G=U1$KSemmAO~f
zX}U~brSsY6;%Q$THqFrwzqtKLJmu=z4|!jIEh_c+{^QN<6)m&hu5Q!x>g_M5MQ@VN
zFZ%+%<F-ETn&<iK_4bcr`CK-BbxAuvAN=ofS2X3;kNbQmA0CPW7}I|IvTKUNZd1)?
z|N3)ZKeu~mO_f|c7u)AxFMg-X)bF@`?)La}tXjj~zHBQo-j7?am+QrR_Tl*S#Xq*b
zPlk8+r9O94dK-63M6;Y9*iH2IQ2cQ$cH5Wa;^)7lc@xTBxtxZ_mAhf<$z5?Mi}M4?
zAHt_%^R+%UmLZ-t55;`;cU9asm)>NL&E=Q6Y3irTrr!UrU-jk5Ki93J<$lVa>qGfh
zy=yjA^3QU&D|Zj!#C}!Yef(1J%clXiRlWW1_wu<&4s~;~P&nj%Q$71dz1}tDl{vB-
zG_Iw3N$#t1zc0St$eH@}pdo5da`#x?H_6?;D842a$Nq%pvybJUMV0jS{M5R_#rxrG
zveXZ0ZSQ9|pNg{fdf^@E<Ds~E{j{&j`_doWyG_ZqPTAF$vPmu;{ZS;}i>gYtoBd{6
zHZMQ<+4sjoSs$O14|Qvhw`J7?Px<x!-p~G6H$F19ZM5)R20J}P+UsvVdLR7Zbn^@j
z@}cg2<Ab9rw#}j5d3U{gJU0G!?f8D+r@E^A&uwh9&-4cKgEt=!b&`3MC~v0BF`xZs
z^R1|g-9z)3T<o5tlY4u<^8nL6^4+1XzZJ=wV&_BOM@03HCqF!GvF`t@q8jZ*KL7v|
CL6(dF

literal 0
HcmV?d00001

diff --git a/tests/data/from_Solis.py b/tests/data/from_Solis.py
index b3a01df55..eff7ffcb8 100644
--- a/tests/data/from_Solis.py
+++ b/tests/data/from_Solis.py
@@ -28,7 +28,16 @@ def test_xpos_ypos_fluorescence():
     assert data.units == (None, None)
     data.close()
 
+def test_kinetic():
+    p = datasets.Solis.kinetic
+    data = wt.data.from_Solis(p)
+    assert data.shape == (10, 20, 20)
+    assert data.axis_expressions == ("frame", "xindex", "yindex")
+    assert data.units == (None, None, None)
+    data.close()
+
 
 if __name__ == "__main__":
     test_wm_ypos_fluorescence_with_filter()
     test_xpos_ypos_fluorescence()
+    test_kinetic()

From acad6c6a8bcd24548cc5cdaa1979346c7fffd396 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 25 Oct 2021 20:18:08 +0000
Subject: [PATCH 6/6] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/data/from_Solis.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/data/from_Solis.py b/tests/data/from_Solis.py
index eff7ffcb8..c29657272 100644
--- a/tests/data/from_Solis.py
+++ b/tests/data/from_Solis.py
@@ -28,6 +28,7 @@ def test_xpos_ypos_fluorescence():
     assert data.units == (None, None)
     data.close()
 
+
 def test_kinetic():
     p = datasets.Solis.kinetic
     data = wt.data.from_Solis(p)